Hi any recommendations on which tour company to us on this day trip?
You do not need a tour company, but can set your own, depending on your interests. Ideas on what you want to see and do?
A tour company that provides transportation to and from Salzburg/Munich? If that's what you mean, its a simple train ride and a short walk to city center.
If you are talking about a tour for Salzburg, you could use Panoramic for a Sound of Music tour and there are a few others, one that uses bikes (Fraulein Maria). You could also use the RS guidebook that has a walking tour for Salzburg.
If you travel to Salzburg on you own, you won't be constrained to venues and the schedule of 3rd party organizers. You can spend as much time as you want to at any venue, and you don't have to waste time at those in which you have no interest, but you have to do a little planning on your own.
I think rail is the most effective way to travel between Munich and Salzburg. There are three or four different trains you can take, regional trains, long distance trains of the Bahn (German Rail, EC or IC), RailJets (long distance trains of Austrian Rail, RJ) and WestBahn (a private company). There is no significant difference, time wise, between the four options. They all take about the same amount of time, and, depending on departure time, any one might get you there sooner.
Regional trains run hourly; EC/IC and RJ run every other hour.
I think the main difference is in the cost. With regional trains, you can use the Bayern-Ticket, 32€ for the first passenger, 10€ for each additional passenger (up to five, total) for a day's travel, ergo, round trip if you do it in a day. The Bayern-Ticket allows you to use any regional train all day long.
Both the Bahn EC/IC and the RailJet cost approximately 40€ (±) each way for a fully flexible ticket, like the Bayern-Ticket. There are less expensive, train specific tickets for these trains, but you have to commit to a specific train (time) and they are sold per person and they are still more expensive one way than is the Bayern-Ticket which can be used for a round trip, at no extra cost, if you do it in a single day. The only limitation is that, for weekdays, travel with the Bayern-Ticket has to be after 9am.
Edit: Jules, you're right. Kind of a double negative there. I was thinking of when it was limited to after 9, but put down when it wasn't.
@Lee, its been awhile, but isn't it weekdays in which the tickets are valid only after 9am?
Look on Viator and Get Your Guide. They will probably have some offers. Enjoy.
As a day trip I think the guide will be money well spent. Enjoy.
Both the Bahn EC/IC and the RailJet cost approximately 40€ (±) each
way for a fully flexible ticket
A fully flexible tickets is for a route not a train, so with a fully flexible ticket you can take the EC/IC RJ and regional trains on the route. The RJ trains are in fact operated by DB till Salzburg, and are internally treated as an ICE, but using an Austrian trainset.
In Germany a flexible ticket allows you to take any train on the route of the category you selected during booking, as well as lower categories.