Not so much railway oriented, but the airplane museum at the Gatow (sp?) airfield is a very large display.

Another place to consider is the museum on the site of the old Spandau prison, which has all sorts of memorabilia from the time of the division of Germany. Not so much for a 3yo, but later in life to remember what happens when things go wrong politically.

if you take the S9 line (S Bhan) from the airport to the center of Berlin then on your left (I think around Schöneweide station) there is an old yard with the round engine shade and the turning table), you can see from the train, don't know if it is accusable.
In the last month I've been in Berlin twice and walked a distance but didn't spot any models shop (really didn't look for them), I guess a Google search will yield results.
Enjoy your visit, very interesting city.

and the Deutsche Technik Museum

https://technikmuseum.berlin/

My visit to Berlin was a bit rushed and the weather was not coöperating, but here are some notes.

The German Technical Museum was a huge disappointment. The railway exhibition AND the old brewery exhibition were both completely closed to the public, for this one week only. They were "rearranging exhibits". There was no warning at the entrance; I only found out after the museum already had my money.

I was only able to visit three model shops.

Michas Bahnhof (Nürnberger Str. 24A) was the highlight. A large variety of second-hand stock. Also a very large variety of toy autos & trucks, including a lot of Matchbox models that I remember from the 1960s. The staff was super helpful. I bought an old Märklin railbus (analog H0) that needed some adjustments, and it was thoroughly tested and brought up to snuff right at the counter.

Modellbahnen am Mierendorffplatz 16 is perhaps a bit larger and has a good variety of scenery model kits, of trackside signals & streetlights (lots of Viessmann), and of books. Also a stand overstuffed with track planning books.

At Turberg (Lietzenburger Straße 51) I was very much in a hurry but it too had a nice selection.

All three shops had a selection of second-hand (already-assembled) scenic model kits, ranging in price from four or five euros to over one hundred for some very nice ones such as large engine sheds.

Also, for gifts for kids I can recommend the shop Die wilden Schwäne (Schönhauserallee 63).

Thanks to all for the tips.