Best Air 1150 CPU Cooler for Mini-ITX Gaming system?

Z97 is a chipset which offers two main features over H97. Overclocking and SLI.
If you don't have a K-series CPU, then the first one of these (as well as the need for a substantial CPU cooler) is void and SLI is redundant on an ITX system. If you are intending to overclock then Z97 is the only option, but you'll need an i5-4690K.

The reason the MSI board is bad is because it locates the CPU socket too close to the PCIe slot. This means that most air coolers are not compatible with the board even though you have no issues with clearances in the case. A closed loop or custom loop water cooling solution won't have this problem, but the largest air cooler which will fit comfortably will probably be a 90-93mm tower cooler OR an awkwardly offset C-style cooler. Pretty much all MSI ITX boards are exactly the same in this aspect.

To the best of my knowledge there is no resource for ITX cooler compatibility. I'm actually working on something myself at the moment as it's a bit of a hobby of mine, but there's a load of information which you need to check to be 100% confident.
I'm a big fan of Noctua because they do check all of their coolers against all of the current generation motherboards and produce excellent compatibility lists which give you a good idea of what sort of size/style will work on a given board.

If you pick a board with a (fairly) central CPU socket like most Asus, ASRock and the more recent Gigabyte boards you can fit the vast majority of large air coolers. The reason I mentioned the NH-D15 is because it's the exception rather than the rule - it's 150mm wide which means it's always going to be overhanging or blocking something even though it is possible to mount on some ITX boards. It's predecessor, the NH-D14, fits on all of the boards I mentioned and by extension coolers with similar dimensions like the Phanteks PH-TC14 should work too.
Now these coolers are the extreme examples, but I direct you to those because anything smaller - be it single heatsink 140mm/120mm fan will fit on those boards without any issue and is probably going to make more sense from a practicality standpoint. Also, notice that neither of those (huge) coolers have major issues with RAM compatibility in the images I linked. Always go for a two stick kit (be it 2*4Gb or 2*8Gb as applicable to your needs) and avoid the ridiculously elaborate heatsinks which might cause you problems.

Pretty much all of the Z97 boards are going to achieve fairly similar overclocking results so it's partly going to be down to personal choice on the list of features.

There's not a lot of Z97 ITX boards so I'll run you quickly through my own preferences.
I'd rule out the two MSI boards (MSI Z97I AC and MSI Z97I Gaming AC) for the layout as previously mentioned.
I'd rule out the Gigabyte GA-Z97N-WIFI and ASRock Z97M-ITX/AC for being fairly sparse on features for Z97 boards, especially for the price (even though they are among the cheaper options).
I'd rule out the EVGA Z97 Stinger because it doesn't have Wifi. It might not matter to you much but it's basically a standard feature on premium ITX board due to lack of expansion.
I'd rule out the EVGA Z97 Stinger Wifi and the Maximus VII Impact as I don't think they are good value. The Impact especially is very impressive, with a huge list of features you'll probably never need but it's incredibly expensive - around double the cheaper Z97 boards price.


That leaves you with the ASRock Z97E-ITX/AC, Gigabyte GA-Z97N-Gaming 5 and Asus Z97I-PLUS. All of these are fairly similar in specs and all within a sensible price range. They should have similar cooler compatibility but I'd check as many sources as possible in advance to be sure. My personal favourite is probably the ASRock as it's usually the cheapest and has arguably the best featureset - it's the only one of the bunch to have both M.2 and SATA Express ports (new interface options) - but there's probably not a bad choice amongst those three.