If you come to Vallarta between December and February and you have never gone whale watching, I would strongly recommend this kind of tour. There are already some whales in November (as they are just arriving) and a few still in March (already leaving) but there are fewer so the chances to see them are lower. I would say February is about the best time because the whales have already given birth to their babies so you can see them too.
There are many companies which provide this tour. We picked one with Banderas Bay tours & travel because our trip advisor told us it was a good company, with a good ship (the Kon Tiki), etc. I thought it was fine, nothing spectacular but the ship was ok, the guide was funny, there was open bar for like half of the trip and they give you as much alcohol as you want (more than I could drink myself LOL). The breakfast was rather poor and it's an ordeal to try to eat on board of that ship because there are no tables and the ship moves too much while sailing towards open sea. One of the foreign passengers told me that the coffee tasted like it was burnt... and yes it wasn't too good. So I advice that you have breakfast at your hotel instead and just take advantage of the open bar LOL. The price was decent and we got a 10% discount because of the travel package we had purchased, so we decided to do it with these peeps, but I think there are other very similar tours and at similar prices with other companies.
We were lucky enough to see a whale with its baby and without much effort. They didn't come out of the water a big deal, but enough to spot them. It was the only whale around (it was already March) so after a while there were 5-6 other boats surrounding her. It was my very first experience and I was very pleased to see these animals, even from far away (the ship is big so you can't approach or touch them at all). They are very calm and don't get scared or nervous because of all the attention they get, on the opposite, they seem to be quite used to it. We looked at them for a good while expecting to see some kind of jump or something, but alas, it didn't happen. On our way back we also saw a group of dolphins (but they never came out of the water, we only saw their fins). They told us it was possible to see sea turtles and stingrays too, but we didn't see any of those.
Make sure to bring something to cover yourself because most of these tours depart early in the morning and the wind can be chilly. However, after 10-11 AM the sun comes out and you will need your cap/hat and sun tan lotion too. It was a fun tour overall and at least we could see a whale -- many people aren't that lucky, even during the peak season.
You will get plenty of chances to purchase this kind of tour -- even the beach vendors will offer you this and other tours, but of course you can always book them with your hotel's concierge (which I would consider safer). You have to go to the cruise ship pier to board the boats (my tour did not provide any transportation but our hotel was only 3 blocks away so it wasn't necessary), and a $15 MXN fee (a bit more than $1 USD) must be paid to access the pier (a sort of maritime tax).
The last time I was in Puerto Vallarta, we went whale watching. It was in a tiny boat but with an experienced guide. For a couple hours we drove around the ocean and whales were swimming only yards from the boat. It was amazing how close they were. It was kind of scary at first but if you need something to do with kids, it's fun for them. I couldn't tell you where we went to do this, but check with your hotel and see if they have any info.
Boarded a beautiful yaught,sailed out of the harbour and were quickly met by dolphins they stayed with us for an hour or more,then in the distance spurts of water and huge tails erupted out of the water thirteen whales of all sizes,it was magical I will certainly never forget the day,a buffet lunch was provided on board lovely food and a super way to see the new year in.