Your profile does not indicate what brand or model of garage door opener you have but there are a few basics that are pretty much universal.
Your wall switch is wired directly to the opener, and it works okay, so you are right to suspect the remotes. You checked the programming and batteries, and the remotes do work some of the time, so the next thing to check for is interference.A remote sends out a signal in a specific frequency, similar to a radio station, and just like your favorite radio station that frequency can sometimes get lost in static if another station or power source interferes with it. When you stand right under the opener, it is like moving your radio to higher ground, the opener has an easier time tuning in and activating the door.Sources of interference I have dealt with are old remotes in a drawer somewhere with something bumping a button, televisions, satellite systems, a change in local phone or power lines, airports, military bases, sprinkler timers, radios, and a host of others. When the failure only happens intermittently, as in this case, it can be hard to find the source. Try to look for any pattern that might help lead you there. For example, does it happen on certain days only, or, at certain times of the day? Did the problem start when you had a new appliance installed, or your neighbor changed his garage door opener?Many service professionals have meters that can help track the signals as well.If no source can be found, or it is found but nothing can be done to eliminate it, some garage door openers have accessory antennas available that can help with reception. Some experimenting, just like you do with your radio antenna, might locate a spot that works more consistently.