Definitely buy bowl tickets through a third party site - buying from our athletic department puts you in bad seats. The companies sponsoring the bowls get the better seats, which they give away, which get sold online. The two schools invited generally get end zone and upper level seats.
I've bought form StubHub a number of times. I've become a big fan of SeatGeek.com now though.
I've had plenty of good results from both. Check TicketMaster also.
SeatGeek.com is an aggregator of the other sites, but checking the other sites directly is worth the effort just to make sure.
Depending on the stadium, club level seats for bowl games are a great way to go, especially if your travel party includes some less-than-fanatic fans you'll want to protect from uncomfortable weather. I did this for our Music City Bowl against Wake Forest and our Belk Bowl in Dak's senior year against NC State. Worth it both times.