These calculations assume that the general ratio of the ce market as 72cr:1ce (though it's fluctuating between 71-73 recently).

So this assumes that you either have an elevator pass or are using mist for the depths. I'll detail later.

I have been recording my total money gained from doing each boss (FSC,Twins,JK) and have compiled some data. Note that the listed total crowns earned is based on doing the entire level (mission) including killing all possible enemies including bosses and destroying every torch/plant in each level/run (does not include minerals, token, or mat values though, yet).

Here is the data for Vana:
7152cr, 7491cr, 8125cr, 7754cr, 8288cr, 7398cr, 7711cr, 7883cr, 8125cr, 7644cr, 7965cr, 7929cr, 7626cr, 7834cr, 7373cr, 8279cr, 7666cr, 8022cr, 8456cr, 7687cr, 7676cr, 7306cr, 7723cr, 7273cr, 7925cr, 8251cr, 8062cr, 8453cr, 7828cr, 7722cr, 7846cr, 8166cr, 7484cr, 7821cr, 7795cr, 8165cr, 8535cr, 7721cr, 7983cr, 7854cr, 7766cr, 8530cr, 7916cr, 8036cr, 8050cr, 7662cr, 7898cr, 7789cr, 7814cr, 7862cr, 7621cr, 7723cr, 7932cr, 8279cr, 8358cr, 8057cr, 7627cr, 8084cr, 7938cr, 8020cr, 7788cr (n=61)

Here is for Jelly King:
2524cr, 2620cr, 2557cr, 2369cr, 2603cr, 2769cr, 2598cr, 2267cr, 2941cr, 3061cr, 2327cr, 2387cr, 2612cr, 2550cr, 2884cr, 2363cr, 2565cr, 3174cr, 2653cr, 2626cr, 3078cr, 2703cr, 2671cr, 2577cr, 2660cr, 2366cr, 2365cr, 2580cr, 2456cr, 2747cr, 2395cr, 2648cr, 2655cr, 2565cr, 2672cr, 2895cr, 2664cr, 2585cr, 2693cr, 2458cr, 2648cr, 2517cr, 2454cr (n=43)

Here is the data for Twins: (for reference if someone was interested)
2512cr, 2583cr, 2789cr, 2441cr, 2490cr, 2205cr, 2451cr, 2454cr, 2569cr, 2946cr, 2605cr, 2330cr, 2446cr, 2738cr (n=14)

Averages based on the data:
Vana = 7881cr
Jelly = 2616cr
Twins = 2540cr

With tokens, you gain 3-4 Bark Modules, 3-4 Jelly Gems or 3-4 Almirian Seals depending on luck. For simplicity we'll just say you get 3 of each per run.

Vana:
3 vana tokens is worth 1000crowns each because you can spend 30 tokens for a 5star ancient item, and then sell that item to any vendor (Basil) for 30k crowns. 30 tokens = 30k crowns, so each token is worth 1000crowns minimum (excluding trading 40 for FOV then unbind + sell but that's a different venture). So to total, in an average vana run, you would get 7881 crowns + 3 tokens worth 3k cr each. So total eventual income would be 10881 crowns per average vana run start to finish.

JK:
Note that the unbinding fee for the sealed sword or antigua (3star) is 600ce. This is about 43200 crowns (600x72) in the current market. It takes 20 Jelly gem tokens to trade for either of these weapons, that is 7 JK runs given you get 3 each time to get 20 tokens for the trade. Sealed swords tend to sell for 40-80k crowns (with no UVs) with antiguas selling for 40-70k crowns. Given you could sell a sealed sword for a total profit of 60k crowns, you would be making a total profit of 16800 crowns (profit - unbind price). Because it takes 7 JK runs to get this profit, each run (3 tokens) would be worth 2400crowns (16800 / 7). Therefore the total income per run of JK would be 2616 crowns + 3 tokens worth 800 crowns each. So total eventual income would be 5016cr.

RT:
The trading and unbinding of the Pulsar or Catalyzer is relative to the AH market (given you are selling it at a fair price, undercutting a common AH price for the item). Based on the cost of unbinding (2star, 200ce) you would have to sell the Pulsar/Cat for over 14,400crowns (200x72). Given you sell on the AH, you lose 10% from the fee, so it'd actually require you sell it for more than 15k. The general selling market is relative, but I most often see pulsars selling for between 20k and 30k. Let's say you sold it for 25k crowns (on a good day). The unbinding fee would be 200ce (14,400crowns), so you'd make a profit of 10600cr. It takes 15 tokens to trade for a Pulsar, so each run (3 tokens) would be worth 2120cr in tokens. That is assuming you sell it for 25k, which is a good day. Most sell for 22k if not less nowadays. Therefore, total income per run would be 2540 crowns + 3 tokens worth 707 crowns each. So total eventual income would be 4660cr.

Results:
So in comparison of total income:
Vana = 10881cr per run
JK = 5016cr per run
RT = 4660cr per run

The amount of income to answer your question is based on time. If you can do two JK runs in the time of one vana run, you're making the same profit (though using more mist).
Given you were running the bosses on full ce, total income would be:
Vana = 50ce (3600cr) - 10881cr = 7281cr profit per run
JK = 30ce (2160cr) - 5016cr = 2856cr profit per run
RT = 30ce (2160cr) - 4660cr = 2500cr profit per run
If you were running on full ce per boss run, you'd have to be able to do about 2.5 JK runs in the time of one Vana run.

This does not include the comparison of heat gained, as well as the materials and minerals. Maybe I'll do one of those comparisons in a later analysis of the numbers.

Sorry for the lengthly post, and hope it helped answer your question.
EDIT: As of the AH currently, the lowest buy now price for a sealed sword is 60k crowns (good guess). For reference of current lowest AH prices (buy now):
Sealed Sword: 60k crowns
Antigua: 77k crowns
Pulsar: 30k crowns
Catalyzer: 28k crowns