Kuja is the infinitive and njoo is the imperative or command. Someone else mentioned, however, that in Kenya, it is common to use kuja as a command as well.
there can be more than one use for the same word, just as 'njooni' and 'kujeni' mean the same thing. It just so happens that the infinitive form of the word is the same as the command (you can't say 'ja!' to mean come). 'Kuja' and 'kula' show up often in their infinitive form because oftheir monosyllabic nature (e.g. 'amekuja', 'tumekula')