score:11
You should be fine.
Early afternoon is not the busiest time in Dutch trains, so there should be plenty of room on the train for both you and your bags. I would recommend taking the direct hourly train from Schiphol all the way to Groningen (departs every x:04), as otherwise you would have to change trains at Zwolle, which sounds like unnecessary hassle just to save half an hour.
Most likely, this will be an ICM train (also known as "koploper"), which is a good thing. These are fairly normal single-decker trains, so you won't have to deal with another set of stairs as in the double-decker variety common on other routes (VIRM or DDZ).
There is no dedicated luggage compartment but (this being the Netherlands) there is quite a lot of room for bikes which shouldn't be full this time of the day, so you can put your bags there. Alternatively, you can take your bags inside the seating compartment and place them either in the overhead luggage racks (if they fit and aren't too heavy to lift) or between the backs of two seats facing the opposite way (this might be only possible in the double-deckers, I'm not sure). The interior of an ICM looks like this.
Note however that formally speaking, your bags shouldn't exceed 85 centimeters in any dimension. I've never seen anyone measuring bags, so this shouldn't be an issue in practice, but if your bag is much bigger than the limit, make extra sure it doesn't get in the way.