Truly and Apizza Doho in Dana Point are my choice for best. Gibronis is worth mentioning for Detroit style. Pizza Port is the best for beer and pizza, the lunch slices always taste better than the full pie and it's an incredible deal if you just want a couple of slices and a brew.
Another vote for Gibroni’s if you like Detroit-style, it’s my favorite pizza around. Buona Forchetta for a traditional Neapolitan pie.
As someone else mentioned, Truly and Apizza Doho up the road are both great with Truly taking the slight edge for me personally.