Firstly, I strongly suggest you to post this in some stack exchange forums for better answers. Because your question doesn't contain any Matlab specific doubt to be appropriate for posting here, unless you have written any code on this.
Secondly, similar to what you said, I would say that you need to work with the frequency spectrum so that you have frequency bins to enable you to take the ratio of magnitude of your signal's peak to rest all other bins. But if your signal is non-sinusoidal then you don't work with just a single peak but rather work with the concerned band. How to do that in terms of simulation can be found here. https://dsp.stackexchange.com/questions/51060/calculating-snr-from-frequency-domain
