Can anyone suggest a travel agent who specializes in booking transportation, hotels and day tours in Munich and Vienna?

Most of the folks on fodors are independent travellers so
you may not get too many answeres here. You can do it easily
with the help of a couple good guidebooks like Fodors or Frommers and the help of the Internet for booking by e-mail.
You could also use Venere or booking.com to book hotels.

The German train site bahn.de can be accessed by the Internet and tickets within Germany purchased over the Internet, if desired. At least use it to get schedules so you know when the trains leave and arrive.

As for day tours, I find Rick Steves gudebooks have the best info. on organized walking tours in English.

If you must use an agent, most travel agency in your own country should be able to help in these two poular countries.

Pat

Marion Harbison is a Conde Nast recommended TA for Germany. She is German but has lived in the US for years. She has encyclopedic knowledge and can be extremely helpful. Email her at [email protected]

Unless you want to go for a luxury trip (with 5* hotels that pay commission and private guides ditto) it is generally quite expensive to have a TA do a trip for you - since they typically charge an hourly rate.

Nytraveller I think it might be a US system where travel agents charge by the hour. They don't operate like that in Australia and possibly not for this OP depending n where he/she comes from. I do agree though that it can be done without a TA.

Although it is best known as a rental car consolidator, I undersrtand that www.gemut.com in Seattle is a full service travel company. If their rental car service is indication, they probably are a very goood agent. In any event, they specialize in Germany and Austria.

regarding day-tours in Munich and Vienna

i recommend after my experience Viator agency

here is the tours options
For Munich :
http://www.partner.viator.com/en/13746/Munich/d487-ttd
For Vienna :
http://www.partner.viator.com/en/13746/Vienna/d454-ttd

for the hotels i will never need an agent , i booked all my hotels via booking.com , and in munich i recommend the hotel below http://goo.gl/7OnCmd , good location , and great price for a city like munich