OP! I completely agree with almost everything on your list. This week alone, i've had Patsy's pizza 5 times...NO JOKE! I had a chick visit me from Australia and she just couldn't get enough of their pizza. I live in East Harlem too, so it's a no brainer.
I tried Lombardi's a few days ago and I just didn't like it much. I may try Joes and see what the deal is.
I would also add a few resteraunts:
Chinese Mirch - 28th and Lexington for great Indian/Chinese food
Nyonya - Spring between Mott and Mulberry for great Malaysian food
Creperie - The most amazing crepes. I like mine with Nutella, Walnuts, and bananas.
Desert Truck - on University Blvd in the East Village (not sure exactly what street). A young pastry chef selling world class deserts out of a truck for $5/pop.
Buddah Bar - When you want to impress someone with a great atmosphere and fantastic food. You'll need reservations, stick around after dinner on a weekend to see real guidos in action.