If you have a TC33D then unfortunately the power steering filter is also the reservoir (the whole thing unscrews) & if it has been contaminated with water I would probably bit the bullet & replace it (NH # SBA3601014700, it expensive..... ($100++)
So not sure how much water you got into the system or how long it has been run that way.... but I think would drain the PS (hydraulic) fluid (there is a drain plug o the bottom)and remove the reservoir / filter. Then I'd open the lines at the power steering hydraulic cylinder (lowest point) to get as much fluid out as possible as ruffdog suggested. I'd let that drain as long as needed...
The problem I see is if it has bee run & depending on how much water got in to the system; I don't believe there is a ideal way to flush the pump, power steering control box or the lines without running the pump.... or complete disassembly. I don't think you can just try to flush with some clean fluid (NH Multi-G 134 or equivalent).... I don't believe it will gravity feed thought the system past the pump but you could try.... (I think the pump will need to run) Another idea is leave a line open & with one person constantly filling the system via the filter reservoir & a pan under the open line start it up & try to purge the entire line till clean.... Never done this but just an idea....