I also stayed at the Comfort Suites Miami Airport North. Not expensive, good free breakfast, and great free shuttle straight to the port. Oh, also a free shuttle from the airport to the hotel (it was kind of late, around 9 or 10 pm, but the shuttle only took about 15 minutes to arrive after we called the front desk). We didn't really explore the area, we just got pizza delivered to our room, but we didn't feel unsafe.
Just a note we didn't fly in, we took a Megabus from our hometown and it let us off at the Miami airport. The bus wasn't real comfortable and the "free wifi" that was excessively advertised didn't work at all, but the fare was so much cheaper than gas/parking would have been. It was clean, on time, and crazy cheap (total fare for 3 from Tampa to Miami and back was like $24, I bought an extra seat so I could bring an extra bag and also stretch out a bit).
I liked the Port of Miami. The terminal is nice and even though you don't get to see a special Disney terminal, all the staff were very friendly and made us feel welcome. It's also very cool to watch the Miami skyline fade away as you sail off.