Katja,
Mozambique is indeed the place to go, in particular Inhambane province, otherwise known as the Manta Coast - Guinjata Bay (Praia de Jangamo), Tofo and Barra.
With one of the largest concentrations of whale sharks in the world, and THE largest recorded concentration of manta rays on the planet, diving off the coast of Inhambane really is world class.
As the poster from Liquid Adventures pointed out, you mostly see whale sharks on ocean safaris in this area, although sometimes you can be lucky enough to catch one cruising past on your safety stop. All of the local dive operators run regular ocean safaris and the height of the whale shark season is the summer months - October to April.
Manta rays are most commonly seen whilst scuba diving at the local cleaning stations, where the mantas come for their vital cleaning rituals. The most famous being Manta Reef, which all dive operators in the area visit and has 3 registered Manta cleaning stations. Mantas are present all year round but again the peak season is October to April.
The winter months - May to September - are when the humpback whales visit and can be seen migrating in great numbers from the southern oceans to northern mozambique and back.
I run a dive centre in this area, so if you would like any more information please visit our website - just google Jeff's Palm Resort, we're at Praia de Jangamo.
Good luck with planning your trip, you're going to have an amazing time!