I would need to know your travel dates/days of the week to provide specific logistical advice.
Which town... both are about the same size and are separated by 10 train minutes, with Bacharach further south,. On most days there are direct trains every two hours between FRA and Bacharach with other options requiring a change of train in between. St. Goar has frequent train service as well but you will normally need to change trains to get to FRA. A minor consideration really unless you're disabled or carrying way too many bags.
In a nutshell: Bacharach has the most attractive old-world buildings (but also more noise than other towns from the passing trains.) St. Goar's buildings are less impressive, but it offers several other important advantages. Its location 10 minutes north of Bacharach by train is more scenic. St. Goar is also better for outings by train and for river cruising. If you're lodged in St. Goar, Rheinfels Castle (which is right in town) can be visited whenever it is convenient rather than having to make a special trip there. Also: a ferry in St. Goar runs all day long and allows you to access the east bank trains for trips to Marksburg Castle in Braubach or Rüdesheim to the south (if you stay in Bacharach you'll need to travel to St. Goar by train first.)
St, Goar Ferry and view from the St. Goar river bank: http://www.schiffbilder.de/1024/personen-fahrzeugfaehre-loreley-vi-zwischen-18381.jpg
So for your independent stay St. Goar makes a little more sense to me, all things considered. You might find it interesting to switch to a Bacharach hotel after picking up your husband at FRA (drop your own bags at the Bacharach establishment on your way to FRA??) Check reviews for comments about train noise.
You might also consider staying in Cochem on the more peaceful Mosel River instead of the Rhine. Trier is nothing at all like Cochem.
http://www.der-takt.de/typo3temp/_processed_/csm_NEU_T_Reichsburg_Cochem_3_087e83a8d1.jpg
Hahn shuttle buses also server Koblenz and Bullay, just upstream from Cochem.
"...you should have sufficient time to get him back to Bacharach, do a cruise to St. Goar (RS tour book has the information), take the train back..."
IMO this is not the best plan; Bacharach to St, Goar is only a 40-minute cruise and covers only HALF the most scenic segment, which actually begins in Bingen. Here's a map of the scenic part:
http://www.bingen-ruedesheimer.com/images/map/rhine-valley290.jpg
If you stay in St. Goar, then on the morning of your departure for Trier, you can take the train to Bingen, cruise back to St. Goar, and see the whole thing by 11 am. Then fetch your bags and head to Trier or spend a little in St. Goar first. Normally there's a train from St. Goar at around 11:30 that gets you to Cochem a little after 2 pm.