Hi Antonio,
I dove with all 3 Tofo dive ops in March 2014. Diversity, Tofu Scuba and Peri Peri are all safe and professional operators. I usually decide on a dive op first and then book accommodations around the dive op. I chose Diversity for most of my dives and enjoyed them. A couple important differences to consider:
Nitrox + bottom time: Many of the best Tofu dive sites are 100 fsw/30m square profiles. Nitrox will increase your bottom time. Free Nitrox at Diversity and Tofu Scuba guarantees other Nitrox divers and a Nitrox guide. In Mar 2014 Peri Peri could not guarantee Nitrox tanks or a Nitrox guide.
Bottom time limits: Diversity and Tofu Scuba limit their afternoon dives to 45 min, while Peri Peri gives divers 60 min. All morning dives are limited by NDL.
Third dive options: All ops theoretically offer 3 dives a day but in reality it depends on how many customers are requesting an afternoon dive. I sometimes had to switch ops to do an afternoon dive. If a third dive is important to you make sure to request that when you book.
Number of divers on the boat - Diversity had the smallest number of divers on the boat when I was there (ranged between 7 and 4 and one day they took me out alone). If you like a smaller dive group, for the prime morning dives you have a better chance of that with Diversity. All ops had similar diver to DM ratios.
Weather cancellations: Generally if 1 op cancels due to sea conditions they all cancel. When I was there 1 full day and two half days of my 9 dive days were cancelled due to conditions.
The Estuary: If you like smaller animals, call or drop by TS and PP as soon as you arrive and find out if anyone is running a trip to "the Estuary". Trips have to be planned around the tides and other divers, but if you get on it early there's a good chance you'll make it. It's too shallow to dive, but was one of my favourite sites. Hairy frogfish, harlequin shrimp, seahorses, regular frogfish, juvenile fish, flying gunard, pipefish, etc. When I visited only Peri Peri and Tofu Scuba were arranging trips there with subcontracted guides.
Whalesharks: I wrote up my experience and that of two friends here
http://www.scubaboard.com/forums/africa/486370-recommendations-tofo-july.html
Re. accommodations and proximity to restaurants, most of the restaurants are on the south end in town, closer to Diversity and Peri Peri. There are also more accommodations options in that end. I stayed at
Casa na Praia (Casa Amarela side) right on the beach and loved it (more info in whaleshark link).
If you are looking for budget accommodation, there are more options on the north end of the beach, closer to Tofo Scuba, including some backpacker lodges with private rooms. Tofo Scuba has a small restaurant and a few rooms since both are sparser at that end. For Tofu Scuba accommodations, make sure to make a deposit in advance. A friend thought he had a place booked but arrived to find out they didn't have a room for him. Everyone I checked wanted a significant deposit to hold a room.
Tofo Scuba does pick ups from the south end. I don't know whether Diversity or Peri Peri would pick up from the north end but you can ask. It's 10-15 minutes to walk from the south end to TS, longer with a large camera.
Other tips:
Marine Megafauna Foundation offers fantastic wildlife talks Mon, Wed and Fri at 6/6:30 at Casa Barry (far south end of beach). I had researched Tofo diving a fair bit and still learned about some rare animals I didn't know were in Tofo. Well worth the small donation they ask at the door.
Hotel Tofo Mar had a very popular half price happy hour on Fridays with live music and delicious fresh fruit cocktails.
Bring a hat. No shade on the RIBs and if you are at a deep or far site, SIs are on the boat.
If you are flying via LAM I would plan some buffer time into your schedule. I was stranded in Maputo overnight (not a scheduled stop in my itinerary) due to a LAM "mechanical problem". Veteran Moz flyers on the plane said it happens all the time. Some LAM flights left early (!), others left hours late.
One of the pizza places and one of the local Moz restaurants delivers if you are too tired to go out. Conventional wisdom is to head to Moz restaurants before you are actually hungry.
Let us know how your trip was when you get back!