There are lots of buses and tube carriages to climb into or drive, and there is also a little play area by the cafe with transport themed equipment and a wooden train set.
Try to go mid week in term time if you can - weekends and school holidays are horrendously busy with school aged children so I think it might be difficult with a toddler getting pushed out of the way by older children. The good thing is that your admission fee gets you an annual pass, so if your DS likes it you can go back several times which makes it good value.
It's very hands-on, but it's not free (unlike many other museums in central London) so I'd wait until he'd appreciate it a bit more. Like you said - the train ride into London and maybe a bus after that will probably be exciting enough!
It is free for kids with a paying adult - a ticket for you will set you back £15 but it is valid for one year so you can go again and again! For a 16mo I'd probably combine with with a visit to a playground or something if you are coming up specially.