Bonsai Museum
We visited last October - a very pleasant morning out. You can do it in half a day and be back in Tokyo by lunchtime. Take the train to Toro; you may be able to get a direct train (depending on where/what time you're starting - we left about 8.30 from Shinjuku) or you can change at Omiya (which is on the Shinkansen line to Kanazawa). Take the east exit at Toro station and follow the guide tiles embedded in the pavement to reach the museum. There are various information boards outside the station. The museum opens at 9 so perhaps time your Tokyo departure to maximise the morning.
There used to be 30 or so bonsai growers/nurseries in Saitama but now only half a dozen or so remain. The map on the home page of the museum (linked above) shows their location; you'll also find a map board outside the station and one or two map boards as you wander the village.
The museum itself has a large bonsai in the lobby, which you can photograph. There is then a display of a dozen or so (super-prime) bonsai (no photographs allowed), together with good explanations of the history and art form. There is then an art gallery, with various exhibits (woodblock prints etc.), all of which seemed to involve bonsai in one way or another - unfortunately, the labels were all in Japanese.... Outside, there is then a display of 25+ bonsai - photos allowed! Next, there is a courtyard with another 50+ bonsai - no photos allowed. However, you will see from the courtyard that there is a balcony overlooking it so, once you re-enter the building from the courtyard, you can sneak upstairs and take a (distant) photo or two. When we were there there were several parties of (youngish) school children - all well behaved (so not at all an issue). I guess they try to get them interested at an early age.
After the museum, work your way south through the village. A pleasant stroll and you can visit the other bonsai nurseries as you go. Some allow photos, some don't. At one, we obviously must have been the first arrivals of the day as, as soon as we appeared, the chap whipped out the large "no photos" sign. The last one of the day (I think # 3 on the map on the museum home page) had a large collection of all sorts of bonsai - and photos allowed.
You should end up by Omiya-koen station, where you can get a Tobu Noda line train two stops back to Omiya station; change there for a train to Ueno/Tokyo/Shinjuku etc. We stopped for an early lunch at a small restaurant near Omiya-koen station but, if you aim to be at the museum shortly after it opens, you can be back in Tokyo in time for lunch. All in all, a very pleasant morning out and, for us, well worth the effort.