I'd go to Zurich. I wouldn't think train fare would add up to $200. You might look on the Deutsche Bahn website and see what the fare is from Zurich to your destination.

Try looking at this airfare site:
http://matrix.itasoftware.com
You cannot BUY directly from this site, but you can enter different cities, dates, allowable # of stops, whether you can tolerate an airport CHANGE, etc to see if a better price presents itself.
Then go to the indicated airline or purveyor to reserarch that airfare (I found found that it can vary up to about $15 on average from matrix' site).

Well, something is amiss here because Lindau is the only place (of any size) in Bavaria that is within 150 km of Zurich airport (1:37 by train, no stops, or 2:10, with 2-3 stops) or Bahnhof.

And Lindau is over 210 km from Munich airport (3:16 by train, 1 change) and over 180 km (2:14 by train, no stops) from the main railway station.

So, presuming your distance calculations were a little off, then Zurich is the clear winner on price and distance.

If you are not going to be near Lindau, then maybe the calculations need another look.

Possibly I should clarify a bit, my final destination will be Sonthofen and there is rail service there. Zurich to Sonthofen is 130 km, and Munich to Sonthofen is 146 km.

The rail is currently 48 Euro from Zurich and 21 Euro from Munich. It is too far out to book right now, I know absolutely nothing about this part of Europe as I have never traveled there. But I thought this would be a great place to start!

Airports near Sonthofen, Germany (from "low cost routes")

Memmingen at 52.58 km.
Altenrhein, Switzerland at 55.02 km.
Friedrichshafen at 60.43 km.
Innsbruck, Austria at 84.87 km.
Samedan, Switzerland at 114.02 km.
Zurich, Switzerland at 130.55 km.

Sonthofen is on a spur line, off the main Munich - Lindau line. There are direct trains from Munich to Sonthofen; from Lindau you have to change in Immenstadt (9km from Sonthofen). I grew up there.

Munich to Sonthofen takes less time than Zuerich to Sonthofen. (Check www.bahn.de for schedules)

From Munich airport it costs EUR 22 to Sonthofen, for you alone. EUR 28 for up to 5 people travelling on the same ticket. The ticket is the Bayernkarte/Bavarian ticket. It is good from 9AM to 3AM the following day. You can only travel on Regio trains, not the fast IC and ICE trains. The difference in time between Munich and Sonthofen is probably less than 1/2 hour.

Coming from Zuerich, you will need one type of ticket for the Zuerich - Lindau hop, and then you can use the Bayernkarte Lindau -Sonthofen.

The slower train Lindau - Immenstadt will probably add 20 Minutes to the trip.But, of course, you have the Zuerich - Lindau leg to add.

Take a look at this option: British Air Boston to London Heathrow and London (same Terminal 5)to Munich. I fly the Denver - Munich route frequenty on British Air and find them quite a bit less expensive than, say, Lufthansa/United Airlines.

Zurich to Sonthofen is 180 km. on the ground, the 130 km may be as the crow flies, but trains don't fly.

The fastest train from Munich airport takes about 2:50 hours with 1 change. All others take about 3:05 with 2 or 3 changes.

The fastest from Zurich airport also takes about 3 hours but with 2 changes, there aren't many each day and the others take 4 to 5 hours with 4 or 5 changes.

Munich is the winner now.

So, if saving $200 is better for you than saving some time and a little inconvenience, then flying into Zurich is best. Myself, I would save the $200, but I travel a lot and do not mind a little extra time on a train.