The consensus seems to be Arenal, for the views, weather, size, etc. And probably morning, because you can often beat out weather or just cloud cover.
Straighforward drive up to the Arenal one; those who want to just ride up and down the tram can do so for a reduced cost (nice views from the top, but pricey for what it is).

We like Sky Trek in Arenal; they have some of the longest, highest lines in the country, beautiful views of the lake and volcano, and the tram ride up is fun and saves you a lot of uphill hiking. We did it in the morning. The guides were great - very fun and still safety conscious.

We had an exceptional experience with Sky Trek in Arenal. Our children decided NOT to go after doing the two practice zips, and one of our guides accompanied them down the tram and took them to the butterfly garden and kept them company while we zipped along. The girls said they had a great time. I worried and sweated the details of when to go, and in the end, the only time available was 2:30 (which was really 3pm) and it was perfectly fine. In fact it was kind of cool because some clouds had formed and the first two zips were in the clouds, which freaked our girls out of the adventure, but added to the insanity of it all for the rest of us. Our guides were fun and professional and clearly our safety, comfort(mental) and experience was of utmost importance to them. Finally, we splashed out for the helmet video cam ($40) which has turned out to be the best souvenir of our entire trip.

If it's raining, I'd recommend not doing it and waiting for clear weather. People we met zipped in the rain and came back again the next day so they could enjoy the views and said it was so much better. We did have our zip experience cancelled once due to lightning, so I guess they allow you to go in the rain as long as there's no lightning around. They let us bring our cameras, we got some great pictures. At the end, they take professional pictures of you on the line, and you can buy those if you want to.

Sky Trek in Arenal is great.. but you could do both. Canopy Safari is one of the best in the Manuel Antonio area, a fun trip and there is a butterfly garden and serpentarium.
Another one that I highly recommend in the Manuel Antonio area is the ADR Adventure Park! Completely secluded in the rainforest, breathtaking views and tons of adventure! There is a tarzan swing, several ziplines, water fall and canyoning rappelling. You can also start the adventure on horseback ride or take a hummer ride. I have done both and personally prefer the hummer, I'm not a fan of horses Arenal and Manuel Antonio are vastly different places, so if your schedule and wallet will allow try both!

I forgot to mention - wear old clothes; we got grease on our clothes from one of the lines that we did. And no short shorts!

skytrek in arenal was great, much better lines and facilities than what we did in MA.