Is the children’s museum near the Boston marathon route? Was thinking about going this Monday but not sure how busy it will be getting in and out of the city with the marathon.

It's not in the marathon route. The children's museum is located in the seaport. Stay off storrow drive and downtown and you should be fine.

I don't think the marathon route goes near the children's museum. I believe the marathon begins West of the city and makes it's way to Boylston St in back Bay. The children's museum is closer to the ocean on the east side of the city. As to how busy it will be I have no idea, could be busy with all the people in town, or it could be not too bad with most of the celebrations happening more towards Copley square.