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The Wikipedia article for San Blas seems to address this(emphasis mine):
San Blas's location was useful and logical, however, because it minimized travel time from Guadalajara and Mexico City without increasing the total distance to the Californias. Also, the area around San Blas had a plentiful supply of hardwoods useful for ship building and repair. Fresh water was also available year round.
The water supply found here was considered important enough to be discussed in this 1870 publication:
The watering place is at the northern extremity of a large open bay south of San Blas the beach is shoal and the casks have to be rolled 300 or 400 yards through the jungle to a stream of water This stream during the spring tides is occasionally brackish but we succeeded in obtaining supplies by immersing the empty cask with the bung in such a position that only the fresh water which of course would be on the surface could enter By rigging triangles with spars in such a position that the boats could go under them to load we succeeded in embarking daily 32 tons of water
North Pacific Pilot: Sailing directions for the West Coast of North America, by J.F. Imray
Upvote:0
Matanchel had been the port of the Baja California Jesuits, with the inland community of Tepic the commercial center. My research indicates that the mercantile supports of the Jesuits had some interest in contraband trade in that area at the mouth of the Gulf: silver flowing from Sinaloa to the English in Jamaica via Panama, the Manila galleon coming in via Cape San Lucas through Cape Corrientes, and a flow of goods to and from Mexico City out of Chacala to Peru.
Galvez put his naval station at San Blas, in between the Jesuit port of Matanchel, and the port of their donors (Chacala) who had ties to Guadalajara and Compostela's business communities. So my guess is that Galvez had an ulterior motive in attempting to suppress contraband trade through Chacala/Matanchel, i.e., to control commerce in Tepic, by establishing a government station at San Blas. And then, in addition, San Blas had all that the other commenters have mentioned: water, wood, proximity to the California peninsula. Yet by all accounts, it was quite deadly for many people to live in, which does seem to warrant a bit more of an explanation.