"Russ - if we don't plan on visiting Trier is it realistic to do a day trip from St. Goar to towns such as Cochem and Bellstein. It looks like it would take around 90 minutes by train."
Cochem, certainly - no problem. Either 75 minutes using the RE trains or 90 using the slower ones. Beilstein would require a bus or cruise boat connection. You hear a lot about Beilstein and it is cute. But I can't say you'll have the extra time for it - all depends on what you have in mind as you head up the Mosel. And I can't say whether a visit there justifies the additional time. Beilstein is only a few tour buses long. There are other fine towns on the Mosel as well. Winningen is a handsome wine town just outside Koblenz on the Mosel train route. It has 25 wineries, some of them very close in. Google Winningen and "Weingut."
"...we would like to go to wineries..."
Like Winningen, the other wine towns have wineries right in town. Boppard has a good number as well. St. Goar, fewer. Here's a list of Rhine wineries. No reason you cannot travel to the wine towns by train and visit wineries. However, not all are open for walk-in tasting experiences. You might contact the local tourist office to see which ones do that.
If you have just one day for the Mosel and are targeting Burg Eltz and Cochem, that alone will take all day (and a very full one indeed.)
Maybe if you take 2 separate day trips to the Mosel you'd have time for places like Beilstein and Winningen as well. Or maybe you just want to base in Cochem AND a Rhine town.
"Between st. Goar and Boppard which would be a better home base it regards to places to stay, restaurants and traveling to Mosel valley?"
Boppard, hands down.
http://media-cdn.tripadvisor.com/media/photo-s/02/e0/0b/ce/severus-stuben.jpg (Severus Stuben)
But St. Goar isn't too far away and has a very scenic setting and a couple of OK places for meals as well. And the ferry. So you could dine in Boppard and return to your St. Goar hotel quite easily. Or from St. Goar you could ferry across and taste at St. Goarshausen's old-city-tower / wine museum.