C'était un plaisir de faire votre connaissance is quite correct. (not 'vos connaissances').
You could use: 'J'ai eu plaisir à vous rencontrer' (faire connaissance implies that you talked a lot, rencontrer could just mean you exchanged a few words)
It is also correct to say "C'était un plaisir de vous rencontrer." but I prefer the former even though both means exactly the same thing.
"Enchanté d'avoir fait votre connaissance." is very common too.
I met a Belgian earlier today. We exchanged more than just a few words; we introduced ourselves and spoke about our fields of study and how many languages we knew. We also chatted a little bit about the linguistic situation in Belgium. Now I wish to send him an e-mail. Should I begin it thus?
[...] C'était un plaisir de faire votre connaissance cet après-midi.
Or should I write "C'était un plaisir de vous rencontrer cet après-midi."?