Given the prevalence of river transport in the medieval (or even earlier) eras, I'd say that the river city is very likely to be a key trade hub. In addition to the access to fresh water, rivers provide easy transport of goods, armies, and the like. There's a reason many cities were founded near or on the banks of rivers. If the city happened to be at or below the confluence of several rivers, it would be a natural spot for a capital, as information and goods could swiftly travel downriver to it. Between the two options, there are nearly no advantages to the second besides access to the sea, which a substantially large river can grant anyway. Consider London, who has a harbor that can service very large ships, including wooden ships of the line (much larger than anything available during your 1200 timeframe).
As for your coastal city, frankly I don't see a lot of good to come from it. You have access to fish, but any wells in the area are likely to be contaminated with salt (access to fresh water was a key problem in sieges in the medieval period). You'd have to build substantial walls to defend yourself, and, unless on a natural bluff, you're building on relatively unsure ground (sand and sandy soils are not ideal for building large fortifications, and the prevalence of water in the area is sure to make things difficult). One benefit you do get is having part of your defensive perimeter cut off front attack by it being the ocean, however, it is a false defensive perimeter, as enemies can still swim or boat in. Unless you're building a city and castle on a bluff, there's no real benefit, and even then, a city on the river can be far more defensible and better.
If I were building defenses along a major river, I'd have my keep built on a natural bend in the river, to maximize the defensiveness of the river as a natural moat. I'd also ensure there was a well or tunnel underneath the keep to supply fresh water from the river or the aquifer that is sure to be present (Aquifer preferred since the soil would filter out a lot of things that could be used to try to poison defenders). You could even build a system that would allow fish through that could be easily caught to feed defenders, but would not allow men through (like a series of grates). With virtually unlimited food and water, your castle will be very hard to take. Add in a healthy compliment of archers, sufficient stockpiled arrows to outlast a long siege, and counter-siege equipment, you'd have a very tough nut to crack. Even if your enemies took the city itself, they could not rule it.