The only thing that would matter to me is the size of the rooms. Geneva has lots of hotels with tiny rooms, unless you specifically book a larger room. The HIX has standard rooms and it's fine for 2 adults. It's close enough to Blandonnet by foot to catch a tram to the center (about 15min). Or you can bus/walk to the airport and take the train there but I still think the tram is the easiest.
But if rates are similar and room size is ok, I'd definitely stay in town of course. Like everyone said, you will have a free public transport card for your entire stay and it's super easy to get to the airport by train or bus.I would even pass on the HIX shuttle.... unless you need to get to the airport at weird hours, when buses are less frequent.