It's kind of an apple to oranges comparison.
Short answer:
The M9i is going to cooler better.
Long answer:
The M9i is an entry level tower cooler, with comparable results to the Cooler Master 212 Evo. It has a TDP of 120w. If you were to compare the L9i to something from Cryorig, you'd be looking at something like the C7. Which I believe still outperforms the Noctua L9i.
The Noctua L9i is a low profile cooler meant for iTX builds. It's going to sacrifice a lot of performance for size. It has a TDP of 95w.
From Noctua's site "The NH-L9i is a low-profile quiet cooler designed for use in small form factor cases and HTPC environments. While it provides first rate performance in its class, it is not suitable for overclocking and should...