Red peppers are usually considered hotter, but sweeter, than green fruits. Here is a thread where everyone agrees on that point. But the heat level often goes along with the stress level of the plant. most of the people on this thread also think red is hotter. If you water only minimally, grow the plant in scorching sun, and are skimpy on the fertilizer, you will end up with some very hot peppers.
This article even says that fruit can get hotter after picking, even when green. Therefore you can choose peppers to use according to the heat needs of the food you are making. Here is a good paragraph to go along with that:
Yes, red jalapeno are hotter than green. Jalapeno chilies progressively get hotter the older they get, eventually turning bright red. As they age, they develop white lines and flecks, like stretch marks running in the direction of the length of the pepper. The smoother the pepper, the younger, and milder it is. The more white lines, the older and hotter. Red jalapeños can be pretty hot, if they have a lot of striations, but they are also sweeter.
And I just found what you could consider almost a duplicate of this post, over on cooking.stackexchange.com:
Are chillies hotter when they're ripe?
The answers to that question correlate to this one, agreeing that the red ones are hotter.
So I would wait until the peppers have colored fully, if you want the most heat possible. The longer you leave them on the plant, the hotter they'll get.
