Mike's Pastry is great, but Modern Pastry is just as good and doesn't have the long lines that Mike's can have. Sticking with the North End Pizzeria Regina is a classic spot. Cheap eats and total locals known is Umbertos. You'll notice it because there is always a line. They close when they run out of food.
Typically Boston and good seafood try Union Oyster House.
Near Fenway Park, and if you are a sports fan Cask n'Flagon.
If you are looking for the typical tourist trap go to Cheers, but don't be confused there are two one off the Public Garden and one in Fanieul Hall, the original one is off the Public Garden.
If you have more questions, ask away. I'm happy to help. I love my hometown!
Everyone's opinion will vary widely when it comes to Boston restaurants. You may want to check out the chowhound.com site (hope that was ok to post?) My current favorites are Prezza in the North End, especially their paella; for pastry in the North End, Mike's, Modern and Maria's are the most popular spots. My favorite is Maria's for the riccotta pie with the chocolate layer in the middle. Anthony's is ok if you just want a lobster, but it fell out of favor many, many years ago as did the No Name. Union Oyster is a great spot for oysters, but make sure you sit at the downstairs bar, if your'e at a table they are most likely pre-shucked. Other favorites are Artu in the North End for thin crusted shrimp scampi pizza or Regina's for a true Boston experience and great traditional pizza. At Reginas, keep it simple and ask for the pie well done, you won't regret it. Hope this helps!