Swimming in the air
I'd say there are two primary limitations, one biological and one physical.
The biological limitation would be whether the whale can get enough food in its natural habitat to sustain its size. This is largely up to you how much they eat and how much food is available. The other limitation is being able to fly.
There are two forces which can keep your skywhale afloat - lift and buoyancy.
Lift is dependent on lift coefficient - which is up to you and depends mainly on shape of the whale and more precisely its wings - speed of the whale and area of the airfoil - which in case of the whale would be primarily the wings, but also its underbelly - and density of the air. With assumption that you don't want your whale to fly at jet aircraft speeds and you don't want it to frantically flap its wings like a bird, it would be fair to treat it - in terms of generated lift - like a glider, which means it would benefit from having large, high-aspect wings (long and thin) as they have a better lift-to-drag ratio and with increased atmospheric density drag becomes a larger issue. There can also be certain natural phenomena on your planet which can increase the lift characteristics which can be utilised by your whales. Thermal soaring, for example is used by both birds and gliders.
It is probably fair to assume that your whale would be unable to support itself with lift alone, which where the other force comes in - buoyancy. It is worth noting that the comparisons to water animals such as actual whales are very accurate for your sky-whale, as we are operating on the same principle in the air - density is what is important.
The closest equivalent i can actually think of are ships. Ships are built of steel, which is denser than water, but float because they encompass a volume of air which is less dense than water. Your whale needs to employ a similar principle. At its extreme, you end up with a baloon full of hydrogen, but you can tone it down to whatever you feel is appropriate. There is a solution that is used by fish to regulate their buoyancy - swim bladder, which you could base your solution on. What you need to do is strike a balance, aiming for neutral buoyancy. Several things to note which will have impact here:
The density of the whale's tissue - less is better. To achieve the largest possible whale decrease the mass (and hence the density), as much as you feel is reasonable. Reduce muscle density to a minimum. Reduce the bones - make them hollow or get rid of them and replace them with lighter structures. There is a bit of a limitation somewhere in there with regards to not letting the whale tissue collapse under its own weight or making it unable to breathe or circulate blood.
Size of the "fly bladder" - bigger is better (in relation to the rest of the whale's body). Whatever you feel will not make it "too much" of a baloon
Insides of the "fly bladder" - the less dense the gas filling the bladder is, the better. It could be hydrogen, it could be some unobtanium or handwavium. Less mass, more volume is better
Atmoshperic density - larger atmoshperic density is acting in your favor, making it easier to achieve buoyancy. If it's not set in stone, you can try to adjust to achieve a bigger whale.
Altitude - atmoshperic pressure will decrease with altitude which means its easier for your whale to fly at low altitudes
In summary, from a standpoint of flight there is no hard limit, but rather it is function of things mentioned above.
By striking a balance such that the whale can achieve a neutral or very slightly negative buoyancy you can make it so that it can use whatever lift force it has available to control its altitude, as well as things such as thermal soaring.
