I have not done it personally, but according to the ASF web site, it does stop at "Como Stazione FS" which is San Giovanni:

http://www.asfautolinee.it/LinkClick.aspx?fileticket=_l-PLYtgZhA%3d&tabid=245&mid=2332&language=en-US

Alternate way to do this from Milano are

1. Take Trenitalia train from Milano Centrale to Varenna-Esino and them walk 10min to the boat dock and take a frequent car ferry or a passenger boat to Menaggio. The car ferry runs late ~10pm. Note the C10 bus stops running around 6pm.

2. Take Trenord train from Milano Cadorna to Como Nord Lago (or Milano Centrale to Saronno, then Saronno to Como Nord Lago.) Walk 10min to Como boat dock, take slow or fast boat to Menaggio. The boats also stop running around 6pm.

I prefer greg's option #1 above. Bus service in Italy is usually very comfortable and reliable, but, for me, there's something special about seeing the lake come into view as you walk down to the Varenna ferry dock and then seeing Menaggio as you cross to the opposite shore. Of course, the bus ride also gives you glimpses of the lakes and towns along the way, but it's just not as special to me.

http://www.navigazionelaghi.it/eng/c_illago.html

Here is the timetable -

http://www.sptlinea.it/LinkClick.aspx?fileticket=_l-PLYtgZhA%3d&tabid=245&mid=2332&language=en-US

The bus stop is immediately outside the station. You can buy the tickets at the bar inside the station - not on the bus.

Since you presumably have luggage the Como - Menaggio option is better than that proposed by Jean. You can visit Varenna once you have arrived.

>>>Note the C10 bus stops running around 6pm<<<

I think it would depend on when the OP is traveling. Your link is for the winter schedule - Invernale 2011-12 (winter 2011-12).

Travelling early May.

In looking at C10 bus schedule from Como to Menaggio, I know that Fer6 means Mon>Sat service. Does anyone know what Scol and Gior mean in terms of service frequency. cant seem to find an answer anywhere.

Gior = daily
Scol = school days