I don't know much about the Boise market specifically, but I have some general thoughts about how I would think about traveling to the same city frequently.
- Given your volume of travel, going for loyaly in one (or even multiple programs) makes a lot of sense. You should have no problem making top tier status which should get you bonus points, room upgrades, free breakfast, etc.
- I would then look at hotel options in Boise to see if one specific hotel or brand of hotels makes more logical sense than another. For example, if a Hilton-affiliated hotel is right next to your work site while the only Marriott is on the other side of town, that would be a big plus for Hilton in my book. Similarly, if the Marriott brand has 5 hotels in town and there is only one Hilton option, I'd favor Marriott because the chances of all of the Marriotts being sold out or charging very high rates during a particular week is less likely than the one Hilton option being sold out. In other words, try to let your convenience drive your loyalty rather than inconveniencing yourself for the sake of the rewards program.
- Particularly if two hotel programs seem similar, consider whether your other travel relationships match up with a particular hotel chain. For example, SPG has a Crossover rewards program where Delta flyers get some additional perks when they stay with SPG (and SPG elites get some recognition when flying Delta). Marriott and United have a similar relationship, etc.
- If you will/can pay for the hotels personally and then get reimbursed by your company, look into getting a credit card from whatever chain you think will become your primary chain. Most cards give you elite or quasi-elite status and also bonus points for spending at those hotels.