You should probably do the complete timing belt service, plus tune-up, etc. You're due. $900 for the belt & water pump is pretty high, but doesn't sound too horribly bad...it's mostly labor, actually. The belt itself is about $60.
$3500 for the complete 90k service is not even close to the right price. I can't imagine the whole service being more than $1000-1200, worst case. Double check that price. Is it possibly they said $350 more, not $3500? $3500 is more like a new transmission price.
Get it done at a Toyota dealer, you'll have Toyota Certified tech work on it, and if there's any issues, it'll be warrantied for awhile. Get it done elsewhere, and it'll be cheaper.