The waterfall rappelling is an incredible tour. You do not need any experience and it is easy. If you are interested, you should do it as it will undoubtedly be the highlight of your trip.
You can book either way. It really depends on how you want to go about it. If you book when you are here and through the operator, you are going to have to go to the office first, which generally would mean an extra trip to town as they usually will not pick you up unless you have paid. You might be able to get a cash discount, but I personally would never keep a wad of cash like that as it would be an open invitation for problems. That said, there are ATMs in most locations, but you would be running back and forth to the ATM daily, which doesn't sound appealing to me either.
Going through a hotel has the advantage that you are staying at their hotel and their reputation is on the line. Therefore, they are going to point you in the right direction to the better tour operators. It should cost the same either way.
The rafting is good in this area. There is also a good tubing tour at The Springs Resort on the Rio Arenal. Hot springs are a must and you may want to do a hike at the base of the volcano.