New Yorkers I need your advice?

Hello. I am from California and need advice on where to stay on the East coast. I am planning on flying into Philadelphia then driving up to Manhattan and then driving to Boston. I need advice on where I should stay while visiting Manhattan. I expect to be their 3-4 days and will have a rental car. I have heard it is very expensive to stay in Manhattan and I am on a budget. I was wondering if their are any cities around the island that are a better option for lodging. Also, I need to be close to a subway and safe.