Well...how big is the scale of this map? If it's all drained by one big river, I'm picturing something the size of the Amazon basin here -- as if you took South America and snipped off everything south of a line between the southern end of Peru and São Paulo. Is that about right?

If so, I'd say you would definitely end up with cities on that series of big bays in the south, probably several -- maybe one at the west-facing one, one or two on the biggest bay there and either the peninsula to its south or the island south of that, and one on that protected peninsula with the big mountain range to its north.

City at the main fork as you said, plus I'd put one on each of the two major forks upstream of that, and one at the mouth.

There is a protected valley in that big mountain range, also seems like a good location, plus maybe something along the length of that river.

Possibly also one on the east side near that island, and another at the east-facing bay guarded by the high mountains. Although...why is the huge west-flowing river draining that whole continent without any mountain range to raise the eastern side? I can't think of anywhere in the real world where a river drains a whole continent without there being a consistent difference in height from one side to the other -- the Andes, the Rockies, the Himalayas. If this were my map I might raise that whole right side of the continent.