I think some sort of light particulate would be better, as the dye would only get one 'pass' or so before it became thoroughly diffused.
I think the food idea is probably the best, as you won't have to worry about cleaning it up as much as some other substance. or maybe some fine grained bits of whatever you are using as substrate.
If you are looking for specific spots, you could try sticking some threads onto the end of a stick/dowel/whatever, and poking that around different areas to try and get an idea of what direction and how fast the water is flowing. Sorta like a movable windsock (watersock?)/flag.