Crates are good for the "time out" that you're describing. Whether or not going in there comes off as punishment will depend on how you do it.
When the boys get too roudy, just announce that it's nap time, get their attention with a treat and lead them to their crates. Put them in, give them a crate toy, close the door and walk away. As much as possible you want them to think they've traded the roudy behavior for something even better--crate time!
What you don't want to do is to scold them, then force them into the crate, slam the crate door, etc---all things that would make it seem like punishment.
When the boys get too roudy, just announce that it's nap time, get their attention with a treat and lead them to their crates. Put them in, give them a crate toy, close the door and walk away. As much as possible you want them to think they've traded the roudy behavior for something even better--crate time!
What you don't want to do is to scold them, then force them into the crate, slam the crate door, etc---all things that would make it seem like punishment.