Why are both Joseph and Manasseh listed as separate tribes in Revelation chapter seven?

How about this, the time of Judgment is ending, so God is my judge, which is what Daniel means is now giving way to "causing to forget" which is what Manasseh means and in order for us to truly rest in beautiful peace in heaven the Lord God will "cause us to forget" anyone who had to endure His judgment of death, while we are enjoying eternal life!

Why are both Joseph and Manasseh listed as separate tribes in Revelation chapter seven?

They are both listed because it fits the meaning of the symbol.

The 144,000 "sons of Israel" are not literal. It is a symbol. For example, it makes no Biblical sense to say that exactly 12,000 will be selected from each of the 12 tribes.

Ephraim has been omitted for the same reason that Dan has been omitted, namely idolatry. Dan was the first tribe to fall into idolatry. Jeroboam placed one of his two golden calves in Dan (1 Kings 12:29-30). These calves served as substitutes for the worship of Yahweh in Jerusalem (cf. Gen 49:17; Judges 18:27-31). And “Ephraim is joined to idols; Let him alone” (Hosea 4:17; cf. 8:11). The 144,000 "have not been defiled with women, for they have kept themselves chaste" (Rev 14:4), meaning that they have not been defiled by Babylon and her harlot daughters (Rev 17:5). So, idolaters cannot be included.

Joseph’s two sons also become ancestors of recognized tribes, taking the place of Joseph. Therefore, right from the beginning, the tribes actually numbered 13; not 12. The number returned to 12 after Levi was withdrawn for the priesthood, and given no distinct territorial inheritance (Joshua 13:14; 14:3-4; 18:7; Num 18:20-24). Consequently, in Numbers and Joshua, the tribes were listed consistently as Reuben, Simeon, Judah, Issachar, Zebulon, Dan, Naphtali, Gad, Asher, Benjamin, Ephraim, and Manasseh. (Both Joseph and Levi were left out).

Levi and Joseph are added back in Revelation to get the list back to 12 because the number 12 is symbolic. It symbolizes God’s people.

There are actually 14 tribes if you consider Ephraim and Manasseh as additional tribes, but this is an abberation in my opinion since Ephraim inherited his father's portion so there were 13. Levi was not given land, his offspring being the priests.

As you indicated Joseph received extra share of land which I suspect is what allowed Manasseh to separate from Ephraim as a 13th tribe. A tribe is essentially a group of people who live together on a single plot of land so by logic if you separate into another plot of land you naturally create a new tribe.

Ephraim however was the oldest and inherited his father's share. Although the oldest son inherited his father's house it was still his father's house and everything bestowed on that house also belonged to the father as long as he was alive (the house was never divided).

Most people today don't realize that. Being the oldest was a mixed blessing. Sure you inherited everything - but that included accountability and responsibility for the house and it's occupants, and deference to his father as long as the father lived.

Interestingly Dan is also missing from Revelations (Ephraim is represented via the mention of Joseph - imho). This makes the count in Revelations back to 12 tribes. Why is Dan not mentioned is a more intriguing question to me.

In context, the list refers to the remnant that was protected from the '6th seal'. Here are two brief commentaries on it:

Resources » The IVP New Testament Commentary Series » 

John's list does not match exactly any of the traditional lists of the tribes of
 Israel (for example, Gen 35:23-26; 49:1-28; Deut 33:6-25), either in the names or in
 the order of the names. Most conspicuously, it is a messianic or distinctly Christian
 list in that it begins with Judah, the ancestor of David and of Jesus, the "Root of 
David" (5:5). Just as the elder's voice had announced earlier "the Lion of the tribe  
of Judah" (5:5), so now John heard a list of tribes announced beginning with the tribe 
of Judah. In each case, however, what John immediately saw was something quite  
different from what was announced. Instead of "the Lion of the tribe of Judah" he had 
seen "a Lamb, looking as if it had been slain" (5:6), and now instead of 144,000 from 
all the tribes of Israel he sees a great multitude that no one could count, from  
every nation, tribe, people and language, standing before the throne and in front of 
the Lamb (v. 9).

http://www.biblegateway.com/resources/ivp-nt/144000-Unnumbered-Multitude

Matthew Henry Commentary
 In this list the tribe of Dan is omitted, perhaps because they were greatly addicted  
to idolatry; and the order of the tribes is altered, perhaps according as they had 
been more or less faithful to God. Some take these to be a select number of the Jews  
who were reserved for mercy at the destruction of Jerusalem; others think that time 
was past, and therefore it is to be more generally applied to God’s chosen remnant in 
the world; but, if the destruction of Jerusalem was not yet over (and I think it is 
hard to prove that it was), it seems more proper to understand this of the remnant of 
that people which God had reserved according to the election of grace, only here we 
have a definite number for an indefinite. 

http://www.biblegateway.com/resources/matthew-henry/Rev.7.1-Rev.7.12

The term Joseph may have been used here as a reminder that Joseph was the actual son of Jacob. Joseph's inheritance was then split between his two sons, Ephraim and Manasseh. As Ephraim received the primary inheritance, his name can be interchangeable with his father Joseph, while Manasseh would require a specific call out.

The commentaries indicate that Dan may have gone unprotected from the '6th seal' for punishment of sin. Tribes suffering various degrees of punishment was not uncommon in the Old Testament. Conversely, changing Manasseh to Dan, all tribes are represented.