I've stayed at both Windsor Hills (2007) and Vista Cay (2008). This year we are returning to Windsor Hills. Really, you cannot go wrong with either resort. They are both very nice.
Windsor Hills is much, much closer to WDW. It takes about 20-25 minutes (without traffic) to get to WDW from Vista Cay. From Windsor Hills, it's only about 5-10 minutes. Vista Cay is right next to Sea World and closer to Universal than Windsor Hills.
Both resorts have gated access, though Windsor Hills has actual guards at the gates. Vista Cay doesn't, you access the property by entering a code at the gate. Windsor Hills also has a much nicer pool. The Windsor Hills pool is larger, has a great water slide, and has the fountains for kids. Vista Cay has a nice pool, but none of the extras. It's just a pool. The club house might be a little nicer at Vista Cay, but the one at WH is nice, too. Windsor Hills also has a great playground for kids, though that might not matter if you visit in the summer. When we stayed at WH 2 years ago in June, it was much too hot to play at the playground. Vista Cay is newer than Windsor Hills, in fact there was still quite a bit of construction going on when we were there in March, 2008.
Bottom line, they are both very nice. If the pool doesn't matter to you (it does to us

), then I would make the location the deciding factor. Windsor Hills is so much closer to WDW. Vista Cay is a lot closer to Sea World, Universal, and I-Drive. Either way, you should have a great stay!