I agree that Spain is a fairly reasonable option in the West Village for good paella.
Underneath the Rock Center is a dining concourse with a place called Cucina and Company. Breakfast and Lots of good sandwiches, soups and pastas for a fairly reasonable price by Manhattan standards. There are tables at which you can eat in the concourse.
Frankly, I'm not sure how the average street deli pops out a bacon egg and cheese on a roll for $1.99 with a cup of coffee. Breakfast at these places is one of the great values in Manhattan. These places are everywhere. But, do move away from the tourist district. You'll get your best deals between Fifth and Sixth Avenue in the 40s (where people work). They're all good and cheap. At lunch, there are pretty good soups and the like. Avoid the by the pound buffets that many of these places have. They're not really a good value nor are they of good quality.
As you head down Eighth Avenue toward Greenwich Village, around 14th Street, there is a great Puerto Rican/Dominican place called La Taza De Oro. Very filling delicious plate lunches for $8-10. You can find similar food and a pretty darn good Cuban sandwich up Eighth Avenue a bit at Havana Chelsea.
Slightly North at Eight and 29 is a great Salumeria that serves very good sandwiches for around $7. All sorts of Italian style cured pork products are available here. Adjoining the retail store is a more formal restaurant. Honestly, I have never eaten in it.
La Taza De Oro
96 Eighth Avenue
Havana Chelsea
190 Eighth Avenue
Salumeria Belliese
376 Eighth Ave
Way North at 110th Street, near Columbia University, really good soul food can be had just blocks from St. John the Divine Cathedral (worth seeing even if fried chicken wasn't in the mix for reasons to go). Mis Mamie's Spoonbread Too serves fresh fried chicken, short ribs, smothered chicken and biscuits, and some of the best sweet potatoes I have ever eaten for around $11-15 a plate. It sounds expensive. But, the portions are both huge and delicious. The owner, Norma Jean, is an absolutely lovely woman, too. It was my go to place on weekends when I lived in NYC.
Miss Mamie's Spoonbread, Too
366 W 110th Street
The Cathedral of St. John the Divine
1079 Amsterdam Avenue
A good morning walk downtown will likely take you past Bubby's and their monstrously large and delicious breakfasts in Tribeca. Go early because the line forms long on the weekends. There will be lots of neighborhood families here, so if kids aren't your thing...
Bubby's
120 Hudson Street
And finally, one of the great dishes that I miss in the mornings in Manhattan are the lemon ricotta pancakes served at the weekend brunch at Good in Greenwich Village. Light, airy and lemony topped only with powdered sugar and strawberries. Mmmm. Delectable.
Good
89 Greenwich Avenue