Alki has more restaurants and probably is closer to Seaside than anything else you'll find in Seattle. Just south of Alki in Lincoln Park is a saltwater swimming pool that's right next to the Sound -- it's pretty cool and might be worth a stop if you're in Alki. I like the beach in Golden Gardens (basically part of Ballard) better because it's not quite so commercial, but it can also be crazy on the weekends. Obviously, given that it's Puget Sound, the waves are miniscule compared to open coast waves. The Washington coast is a pretty long schlep from Seattle and my bias for the Oregon coast is strong -- in other words, despite living in Seattle I drive to Oregon for my coast style beach fix.
I actually like both zoos and don't think you can go wrong either way -- I'd probably go with whatever is most convenient. I live a block away from the Seattle Zoo and go all the time -- feeding the giraffes (10-11 am each day) is the high point for my two year old son. You can usually park for free at the Woodland Park/Seattle zoo if you look about 2 blocks west of the zoo (don't tell my neighbors I said that). If you want a solid burger before/after, Red Mill is about 10 blocks north of the zoo on phinney ave.
