I like Emory, but if you are going up Pinnacles anyway, you might as well just try to do the the South Rim Loop instead. If you have hiked Guadalupe Peak, you can probably manage the loop (Basin->Meadows->South Rim->Boot Canyon->Pinnacles->Basin or the reverse) as a full day-hike, assuming the weather cooperates and you start shortly after sun-up. It is slightly less than 13 miles. Emory is cool, but the South Rim is the showpiece vista in the park, and you definitely want to make it there if you can. The first three to four miles are moderately strenuous, (and you have to do them anyway to get to Emory) but are less taxing than Guadalupe Peak, and the going is fairly easy for the last 3/4s of the hike no matter which direction you go. I have done it as a day hike twice, albeit with more daylight and slightly warmer temps than you will see. Be sure to carry enough water, it is a 6-8 hour hike, with some strenuous sections.
Your daylight margin is thin in January; if you get off to a late start, be ready to switch to the Lost Mine Trail/Window combo (make sure to take the side trail near the Window pour-off for the best view). Lost Mine Trail is the second best trail in the Park, with fantastic views for most of the way and a big payoff at the end. It is definitely a cooler hike than Emory, unless you are the kind who derives a lot of satisfaction from getting to the highest point (and who isn't?)
The Ross-Maxwell Hwy. and the trails along it (Santa Elena Canyon, Mule Ears, and Upper Burro Mesa are the major ones, though there are a lot of cool shorter ones too) combine for a great full day itinerary with very scenic driving between trails, and allows you to tailor a day toward people in your party who are not be as interested/able to hike longer trails. There are numerous overlooks, and great views of the west side of the Chisos (the Window side). Santa Elena is cool and short, and is scary for people who are afraid of heights. Aside from Santa Elena, the trails in this area are desert floor hiking (as compared to the cloud forests of the Chisos). The terrain is more interesting than that suggests, with a lot of variety in landscape, but the vegetation is much sparser and thornier in this part of the park than in the mountains. (Winter is a good time to hike on the desert floor.)
If by Boquillas, you mean Boquillas Canyon: the hike is cool but short, and eventually just peters out rather than coming to some definite end (same with Santa Elena). Not to say it isn't a worthwhile hike, it is a very cool canyon, but I wouldn't let it influence my decision on where to stay. If you are at RGV already, it is worth doing and very close. I haven't been across the river to Boquillas the town; you pass the crossing on the way to the canyon trail.
If you are going to be coming in through Alpine anyway, you could easily just stay in Terlingua/Study Butte every night. Ross-Maxwell is convenient from that side. The Basin is an hour and a half or more away, but if you committed a single full day there, you would only have to make the drive once. There are hotels of varying quality (mostly medium to low) and pay camping spots with showers and other amenities in Terlingua/SB, though most of the private campsites appear to be of the graded gravel lot variety.
As long as we are talking about scenic drives and being on the Terlingua side, don't forget about 170 from Terlingua west along the river into the State Park. Ross Maxwell is the most scenic drive in the National Park, but 170 is the best in the region (IMO, of course). There is great access to the excellent Contrabando Dome system of trails near Lajitas, and a couple of really cool mile long hikes further upriver (Closed Canyon and the Hoodoos). If I had to choose between doing 170 and Ross Maxwell for a day of scenic-drive-with-day-hiking, and I was already in Terlingua, I would definitely choose 170. There are several good State Park car camping sites along the river on 170 that are probably available if you decide to spend time in the area, but they are too far away to use as a base for going to the National Park.
