We stayed at the Tudor Hotel and Suites in Miami Beach. Its about a block from a beach and was such a nice hotel. The rooms come with either a king sized bed or two full sized beds. They have a nice sized bathroom and each romm has a kitchenette (refridgerator, stove, etc.) We booked through Expedia and paid $88/night. They are located at 1111 Collins Ave. Also, they are a short taxi ride away from the pier. They're website is www.southbeachtudor.com you can see the rooms (parts of the hotel are still being remodeled) but don't book through them because they are MUCH more expensive.
I have booked at the Best Western Marina Park in downtaown Miami, the closest hotel to the pier and across from Bayside Marketplace. I have heard good things about it and I am hoping that it lives up to its expectations. It was $84/night Bayview Room thru Expedia.