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In Sanskrit, from which these names ultimately derive, there are three sibilant sounds: one is like the s in sound, another like the s in sugar, and the third is harder. The difference between the last two have disappeared in many modern Indian languages (though, in some contexts, it gets replaced by kh: think the relation between the two pronounciations of ch in different German dialects), and both are usually transliterated as sh.

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In any case, the female name manisha (manISA, मनीषा) uses this hard sh, and is a very old word: it is the root man- meaning cognition (mne- is its cognate in the Latin language) with a suffix. The male name manish (manIsha, मनीश), on the other hand uses the softer sh, and is a modern concoction: the ending -a sound of Sanskrit having disappeared, one was free to add Isha (master, from a root meaning to possess) to get this word.

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Of course, since the sound difference between -S- and -sh- has disapeared in many languages, I have seen manIshA (मनीशा) as a female name as well. I surmise that arose out of a variant spelling of manISA. Similarly, in many modern Indian languages the difference between the short -i- and long -I- has also disappeared, leading to further spelling variants.