Answering my own question:
For Fortaleza - the taxi booth is very organized, and you can easily get the coupon and the rate to different parts of the city is well organized.
From the city back to the airport, it is based on the meter and from Praia de Iracema. Normally it is approx 35-40 BRL.
For Natal: This is certainly a white elephant airport. It is very far from the city center or from Ponta Negra. Since I arrived after midnight, there are not much choice but taking the taxi. I went up to the departure level (looking for an ATM) and from there you can get taxis. Normally it should be approx 100 BRL to Ponta Negra.
From Ponta Negra it will cost approx 80 BRL (no meter used), but I think it can vary between 80-100 BRL (depends on how good you know your stuff).
It takes about 45 mins to the airport or less (if you have a wannabe F1 taxi driver). There can be different variation to get to/from the airport. On the way from the airport, I was a bit worried as the driver went through small villages which seemed dicey, but on the way back to the airport, the driver used nearly all main roads.