There's really nowhere to put large bags on the Vistadome (which isn't a dome like you get in North America....)
Nonetheless, there are no above seat racks (windows run along the sides of the carriage roof).
I did recall some pax taking their bags with them which the crew put in the exit (pair of doors in the centre of the carriage - only place to put them) so you can imagine space is limited.
On the other service, there is, IIRC, space between seat backs and racks at the end of carriages.
What we did was to drop our bags at the hotel in Ollantaytambo before we boarded the train, and came back after an over night in Aguas Calientes.