Bonjour and merci day trips out of Paris advice needed

None of the places you mention require bus travel except Giverny where you train from St. Lazare station to Vernon and then move as quickly as you can to the shuttle bus to Giverny which is there to meet the train. This thing does fill up so move fast; you pay the driver for a round trip ticket. Most people who get off that train in Vernon will be doing the same thing.

For Chartres and Versailles you just take the train and walk; it is easy. From the RER C stop at Versailles Rive Gauche you just follow the crowd; it is about a 15 minute walk. The key here is to get there at least half an hour before the chateau opens with ticket in hand. That gets you fairly far forward in the security line and you won't need to line up for tickets inside. It has been awhile since I traveled to Chartres, but same deal; you walk from the train to the Cathedral which is visible at a great distance. Again most of the people who get off there will be making the same walk.

Note that your train tickets on the RER include travel via metro to the RER station; with the work being done on the RERC in summer you may have to get to Javel station which is easily done by metro. Pick up a free metro map on your first metro trip so you can plan trips easily.

I would never take a tour to such easy to visit places but you should do what makes you comfortable.

Versailles is pretty much a suburb of Paris and easily reached by the city rapid transit service. Giverny does involve a conventional train ride but the shuttle bus is right at the small station (or you could just walk to the gardens.) Can't speak for Chartres. Google Maps is growing more and more helpful in plotting these excursions. Practice on the site before leaving home. I realize I have jumped to the conclusion that you will be armed with some sort of Internet connection: Smart phone, ultra computer, or whatever. If not, your hotel may have a free computer in the lobby. To plot ticket prices:
https://en.voyages-sncf.com/en/

https://www.ratp.fr/en

www.parisbytrain.com has helpful photos of train stations.

I went to Giverny in May and there were three buses waiting for the train that I took and the third bus was not completely full and all passengers from the train were able to get on a bus. Second, there are Monet's water lily painting inspired paintings of footprints from the train station to right outside of the train doors to the bus stop and the bus is a shuttle that runs from the traint station to the gardens -- how easy is that? You should do what makes you comfortable and if you want to take some kind of organized tour from Paris to Giverny, you should do that but getting from Paris to Giverny is so easy even with the change to a bus that I think that a tour is a waste of money. As said below getting to Chartres and Versailles is even easier. I mean at Versailles you get out of the RER C at the Versailles stop and walk 5 minutes or so and you are at the main entrance to the castle. I have not been to Chartres in a few years but I do not recall needing a bus to get to anyplace that I wanted to see there. Probably, the most helpful thing for Versailles is to pre-buy your ticket and buy a ticket to the Kings Apartment Tour so you can avoid lines. I'd do the same thing for Giverny.

Of course, you will have to get to the train (RER or SNCF train) that takes to your destination from Ile St. Louis and perhaps that is the train change that you are referring to, but even if you took a tour, you would probably have to get from wherever you are staying to the starting point of the tour. For example to get from Ile St. Louis to Gare St. Lazare to catch the train to Vernon, I would probably take bus 24 to the train station or walk around 20 minutes to Chatelet and take Line 14 from there but you may not feel comfortable with that so you might take a taxi for that part of the trip. But I get it. If you don't feel like having to get or do not feel comfortable with getting transit schedules and changing metro lines or figuring out which track your train leaves from once you get to Gare St. Lazare of Gare Montparnasse or things like that, then take a taxi to a tour meeting point and get on a tour. It's your trip and you should do it in the way that will be most enjoyable for you.

In Chartres it's a 5-10 minute walk from the train to the Cathedral. You can see the towers from the train station. Easy-peasy.

You might want to book a guide for other reasons, but not for transportation.

Catching the buses between Giverny and the train in Vernon is ridiculously easy (both ways).

In Versailles, some people choose to visit the grounds first, saving the palace until afternoon. If so, there is a city bus from the train station that will leave you off near the entrance to the Petit Trianon. This is a little less straightforward, though I would argue still doable even for a newbie.

However, most people see the palace first, the bust does not save you all that much walking, and anyway there are other options for getting around on the grounds, such as renting bicycles or an electric "train."

in Chartres, the walk from the station to the cathedral is not far. There might be a local bus, but otherwise I'm not clear on why a bus enters into things.

Isle St Louis is tranquil, enjoy your trip.

If you have any mobility issues, I would book half-day bus tours.
Some people aren't used to mass transport, or have health issues, so it would make sense to book an air-conditioned bus.
No sense in getting any more stressed out than you have to be.
For Versailles, go to the official website and book the Private King's Apartment your. You'll see things that others won't and will benefit from a dedicated Pass entrance - but will have to go through Security.
Don't try to see Giverny and Versailles on the same day.