MAUI! Check out Ka'anapali Beach, it's perfect for parent and kids alike!
We've been a lot, and we took my DD when she was 2. I was afraid of the long flight from here, but she actually did better than we did.
Take a portable DVD player and oodles of snacks and activities. Kids that age think it's an adveture going in the plane.
We went to Atlantis this summer and my 5 yr old loved it but we {DH & I} HATED it.
We had horrible service consistently there, no one seemed to care that we were there or not. Restaurants were closed early, they didn't serve food/drink by the pool after 5pm although pools were open until 8, etc. . .
I could go on and on and on. . . .
If he's not a big swimmer, he won't get much out of Atlantis at that young age. It's like a big waterpark, 4+ is probably ideal.
I personally wouldn't go out of the country, customs is HELL especially w/ a 2 yr old.
We stood in Customs lines for 3 hours just in the Bahamas airport alone
Also, San Diego and Seattle are pretty great.