Oh, this is very new to me. South and north of Vallarta in some small rivers are wild crocodiles. But there are always signs warning about.
Each year there is an accident but this is because locals visit these areas without respecting the warnings. Children are running around, playing in the water and so on and more or less yearly something happens.
I never heard that in the turistical areas something happened. The only story I know is about an accident on a golf course, where during the rainy period an area coverted into a lake and a crocodile took his home there, than, when turists was playing during the night with some alcohol in the water of this unplanned lake, the crocodile attacked. No deaths so far.
So, as long as You are not looking for the one and unique wildlife experience, You wouldnt get in touch with the crocodiles.
But if You want to see them You can visit either the zoo or better the CUC local University, as they hold some of the crocodiles there for their studies.
If You want heavily wildlife, You may stay in Yelapa Beach a few days or the Las Animas beach, there You can rent a palapa and You will have everything from spiders to scorpions, snakes and what ever.
I amhere about 5 years now, and out of my view Puerto Vallarta is a very good and safe travel destination. But beware of the sharks ! No, not the animals ! The timesharing sharks. They have in each corner a stand where they invite You to tours and hotel stays, if.., only if You visit their facility where You assist at a "info meeting" about Timesharing. Psychologists (from US and Canada) will "explain" You, why You must have a timesharing contract.
This is the real danger here for first time visitors !
Godd luck, for more info, just ask.