Aegean to West Mediterranean Passages
Depending on the time you would like to complete the passage, your departure point, and personal preference you must decide whether to take a southern route via Malta (south of Sicily) or a northern route along the Messina Strait in Italy (north of Sicily).
In general the northern route is shorter and faster than the southern. Also the northern route has shorter legs and more places to stop.
All the routing instructions described in this page can be reversed and equally apply for passages from Gibraltar to the Aegean Sea (see also the East Mediterranean Passages
The months to be avoided for this passage are from November to April when violent storms are possible.
The best time of the year for this passage is either in May - June or in September - October when various ports and marinas are less crowded and the weather is usually benign. In October, however, there is a possibility of thunderstorms so one has to be cautious.
See the World Cruising Wiki's section for full details