I wouldn't bother with public transportation for such a short trip, especially as the SL doesn't go right to the hotel.
UberX would be the cheapest option, but it might take a while to get a car at that time of night if you can find one at all. There should be plenty of Uber black cars available, but that would cost a lot more. However, both could have surge pricing at that time (holiday, Friday night, winter). Surge pricing is based on neighborhoods now, so drivers might not sit around Logan if they could make more driving downtown.
I would check UberX at baggage claim, and just take a taxi if a car is not around. The tunnel toll is $5.25 and Uber adds another $8.75 ($5.50 as an uber fee, $3.25 to cover the airport limo surcharge).