Ultrashort answer: Little Empires want Science, Big Empires want Gold.
Semi-Short answer: Look at the science slider, the lower you are running it the more you want to prioritize gold over science. Personally, around 40-60% I value gold over science and science over gold if I'm running it higher than that. This is in a CE-style economy with the odd specialist. In straight specialist economy the slider matters much less, so more or less only run enough specialists to keep you out of the red especially since you won't be running US so can't dump excess cash into hurrying stuff. I'd run merchants in your Wall Street city and Scientists everywhere else.
LONG Answer:
You also have to keep in mind the split in technology paths concerning Gold and Research around the middle ages.
There's
Guilds + Banking (which gets you +75% to gold, knights, health cap increase, and gets you started towards rifles)
Education (which gets you +25% to science, Oxford, and positions you for Liberalism)
Astronomy (which gets you +25% to science and opens up overseas trade routes)
Paper + Divine Right (for University of Sankore and Spiral Mineret)
which one you want to prioritize depends on your current situation.
I'd say that Paper+Divine Right is the best from a pure economic standpoint for huge expansive empires, but requires wonder-building and does little for you militarily except get you close to nationalism. The more cities you have the more opportunities you have for +2 sci and +2 gold. Plus Monastaries and Temples are much less taxing on the hammers of small new cities you get through expansion than stuff like Universities or Banks.
Guilds to Banking is a lot better for the military side of things and almost as good for paying the big maintenance cost that big empires require. That +75% bonus to gold is gotten for a lot more cheaply tech-wise and hammer-wise than an equivalent bonus to science. However such a bonus does little for you if are already running the science slider fairly high (small civilizations).
Astronomy is great if you have a coastal empire with a continent overseas. The overseas trade can be HUGE, plus can give you luxury and health resources. A lot of times with an island start, astronomy will slingshot you back to parity and beyond. Just make sure other civs aren't running mercantilism because this will kill it. Likewise you can encourage mercantilism in your neighbors if you want to make sure an island opponent can't take advantage of overseas trade. I did this last game on Emperor to keep the Incas backwards and impoverished
Lastly Education is great if you have a good commerce capital running Bureaucracy with some settled scientists, plus gets you a free tech if you think you can beat people to Liberalism.
Basically, whether you want to run scientists or merchants specialists depends a lot on what economic tech path you're going (which depends on your civ). I'd say if you go Education first, you definitely want Great Scientists. The later you go education compared to banking the less attractive Great Scientists become compared to Great Merchants.
However, considering the academy and Oxford (the fact that it comes significantly earlier than Wall Street) it seems to me that it's much easier to concentrate +% sci in a single city. You can get +200% to sci in a single city as soon as you hit Education (plus more with monasteries), but it's just that ONE city. Everywhere else is going to be sitting at +50-70%. However, +100% to gold can be spammed all over the place as soon as you hit banking, but you gotta wait till corporation to hit +200% in one city. Your single city gold modifier will never be good as the +225% sci modifier with the academy (climbing to +250% with labs).
To sum up the previous paragraph: It's easier to concentrate really high +%sci in a single city than it is to concentrate really high +%gold in a single city. However, it's easier to get a respectable +gold% (100%) throughout your whole civilization than it is to get a respectable +sci% through your whole civilization.
Since Science specializes better, I'd say that it's better to settle scientists in a science city than settling merchants in a gold city. However great merchants give you +food so that is something to keep...
Oh god, this could go on forever. I'll just shut up now.
Something else I forgot. If you are running a SE you want Philosophy. Since that goes well with Education for Liberalism, I'd say that makes Education and thus Great Scientists the better choice, all things being equal.