Hi B.,
This is a very common occurence with toddlers, esp. once they have tasted the freedom of a bed. As I still nurse my son and we cosleep at night, I can tell you that naps are tough some days. He likes to nurse and may fall asleep on the couch or the bed in his room, but more often just wants to pop up from nursing and play. I might then go out for a walk and he'll nap in the stroller.
I've also nannied for lots of toddlers who needed help during nap/rest times, and here are some ideas that have worked.
Laying down together: I notice that you don't want to turn this into a habit, but it may be key for your son to get some sleep. This is very different from his not being able to fall asleep by himself; it's more about his having companionship and "not missing out" on what's going on out there with mom and sister. Some parents just choose to do the laying down on days that their child really seems tired and to give them some quiet time on other days when it seems less necessary.
Quiet Time- is just that. Sitting in one's room and playing and talking up a storm is still quiet time. Looking at books or books on tape is another thing that helped. The idea is that he needs to have some time of day with no interaction so that he can wind down and relax. Some little kids often start to drop their naps around this age, too, and quiet time gives us a much-needed break.Usually no more than 20 minutes before they wander out to find us!
Use a timer--Have him help to set a timer for Quiet Time in his room and then refer back to it if need be. "(He) can come out when the timer goes ding." (Checking in over a monitor can also help, so you can remove the timer if he falls asleep, thus ensuring it won't wake him up.) Practice using a timer at other times of day, and start with smaller stretches of time so that he *knows* it will eventually go off...five minutes can seem like a long time to a little person.
Have a rest time routine--you likely have an evening routine and rest time should be no different. Two or three stories and a few songs, some snuggle time are all ways that we help our children relax to rest.
Adjust his rest time--he may not be tired enough at his usual naptime. Consider moving it back enough for him to have played himself out. If he falls asleep after 3 or 4, a 20 minute catnap can be refreshing while not providing so much sleep that he stays up late. I've regularly woken children after 20 minutes at the parent's request and found that if we had about 20 minutes of stories or some other pleasant activity when they woke that we did fine.
And last of all:Count your blessings-- hey, at least he is staying in the room. That's pretty amazing at this age!