Using Swiss pass and Bayern ticket to get from Zurich to munich?

The Bayern Ticket does not include the little finger of Austria that you'll need to cross. You can choose to take the longer path and stay totally in just Switzerland and Germany and use your current tickets...or you can just buy a cheap little ticket to get you across the tiny bit of Austria which will reduce your travel time.

There are some direct trains to Lindau from the ZRH airport station - like the 9:28 EC 193. There are lots of other options that require changes of train (find them at www.bahn.de.) Then from Lindau, use a Bayern ticket on regional trains to get to Munich. After a 50+-min layover, the connecting ALX regional train from Lindau to Munich is direct and gets you there at 14:41 for a total trip time of just over 5 hours. But you will also find 39-Euro advance-sale tickets for ZRH airport to Munich on some trains - depending on your travel dates and whether the discount tickets have sold out yet - at www.bahn.de . For example, on Dec. 6, there are 7:28 and 9:28 departures for DIRECT trains to Munich for this price - and the trip is just 4 hours.
You could save your railpass day on your Swiss pass this way too - which might be just as valuable as saving a few Euros on the Swiss pass day + Bayern ticket option.

By the ferry, I assume you mean the one from Romanshorn to Friedrichshafen. Ironically, you would avoid having to buy a point-point ticket through Austria but you would have to pay for the ferry and need a point-point ticket (€3,90 pP) from Friedrichshafen, which is in Baden-Württemberg, to Bavaria (if you already had a Bayern-Ticket, €5,30 to Lindau if you were going to buy the Bayern-Ticket there). On the other hand, Switzerland (St. Margethen) to Bavaria (Lindau) is only €7,40 per person Russ's plan, if you can get a Europa-Spezial ticket from Zuerich Flughafen to Munich for €39 per person, saves you €29 for the Bayern-Ticket plus the point-point ticket across Austria, but if you need public transportation once you get to Munich, it's not included with the Europa-Spezial ticket like it is with the Bayern-Ticket. If you want a Bayern-Ticket before you get to Bavaria, you can get it from the Bahn website. Put in any two stations in Bavaria, just so it shows the Bayern-Ticket, and order it online. The Bayern-Ticket is valid for everyplace in Bavaria, so it doesn't matter what two stations you use in ordering it, just the date.

Thanks for all the help. We are traveling with six children so the savings using the regional passes are significant. But, I think the Europe special tickets are worth it just to avoid changing trains so many times. On the way back to Switzerland the only the special tickets are on the very early train. I see that the normal fare for 5 of us is 140 euros, can I use my swiss pass as part of the fair and bring the price down? Thanks

"can I use my swiss pass as part of the fair and bring the price down?" You can of course use your Swiss pass to travel within Switzerland as long as you can spare the railpass day to do so.