The Chicago Manual of Style, 14th Ed. says that "So far as it can be done without confusion,...form the plural by adding 's' alone."
This is also consistent with what I know of all the better technology journals. A lot of technical writers/editors can be neurotic about it, insisting that the use of an apostrophe is an egregious infringement on good taste and a marker of inadequate education.
Therefore, I say choose "GPSs."
That being said, this truly is a matter of pure style. It is not clear to me that there is anything patently "wrong" about using the apostrophe-plus-s method to make acronyms plural. And as such, the values of consistency and clarity should be overriding.