Does anyone know if it is better to book a hotel (Los Lagos) directly through there website, or go through Arenal.net? Is it the same price? What about reliability?

I'd go direct.
If any problems arise with booking etc. upon arrival or checkout the hotel will be responsible and not the agency which is "somewhere online."

I would say, skip the middleman and go directly to the source if you can. As earthtraveler said, "if any problems arise" there were only be one person to blame.

Arenal.net and monteverdeinfo.com do have offices but it could turn out to be a he said, she said if there is a problem. I have read of a couple recently.

both those websites are under new ownership and problems have been reported book direct!

Contacted Arenal.net and found that they were very pushy about hotel reservations & making "tour" reservations, and when contacted by friends traveling with us were told that certain hotels were booked, even though reservations were still available directly through the hotel

great website, useful information, but I would personally book directly with the hotels