There is a great hole in the wall at the corner of 28th & A in Golden Hill... GOTHAM CITY PIZZA... that makes Authentic NY Style thin crust pizza and Philly Cheesesteaks.
Gotham has a very large delivery area, but I don't think La Jolla is covered.
As an ex-NY'er, I prefer the pizza at Luigi's (25th St in Golden Hill) to Bronx Pizza....the owner used to work at Bronx before opening up his own shop...sells pizza by the slice as well as by the pie.
There's also Basic Urban Kitchen & Bar on 10th and J in East Village of downtown that sells Connecticut-style, pan thin crust pizza that is very good.
Z Pizza in UTC in the Ralph's shopping center has good thin crust pizza. They have all kinds of pizza topping combinations, all of them really good. They even have a dessert pizza made of Fuji apples and cinnamon, which I've been wanting to try but haven't gotten around to it.
I've tried all the best thin crust pizza places in SD: Bronx in Hillcrest, Hoboken in PB, and Ciro's in Gaslamp.
A very good (but not in the top tier) thin crust pizza is Regent's Pizza just east of the 5. They delivered to me at UCSD. They do a pretty good job. I took particular note of their sauce, which is NOT canned and tastes very fresh.
The only reason why I don't go to them is because they are pretty pricy for a college student like myself.
Here's the website: http://regentspizza.com/
Hope this helps!