Mmmm... that's a tricky one. I can't really think of a direct translation for the "accommodating" word. The term acomodaticio does exist in Spanish, but sounds too "learned" or "elevated" to say in a regular conversation (at least to me).
For the case you're describing, I (Spaniard guy) would go with something like:
Muchas gracias por adaptarte a mi[s] horario[s].
Someone asked the same question in Wordreference. The last answer (the one the link points to) is the best one in my opinion.
EDIT:
As kelmerkelmer pointed out in his comment, another fairly common expression you can use is:
Gracias por ser tan flexible
This expression goes pretty well when talking about schedules.