torontokids, 3 weeks is not enough time for a part time (2 day a week) to adjust to your nap routine. It might take months. It will happen, but it's going to take a loooong time as he only is there for 2 days a week.
I'm going thru a similar situation. I have a pt dcg that started 2 months ago. She comes 3 days a week. She has recently stopped crying at naptime and now runs to her playpen at naptime. She sometimes will call for me for a good 30 min. But knows the rules (she's 2 yrs). Then she will fall asleep.
Since you have a new baby starting, this is going to disrupt naptime even more. You have to decide if you want to tough it out or terminate. Is the crier in his own room or sharing naptime with others in the same room?