where does the saying originate

Possibly a substitution for "cup of Java" another expression coming from a coffee source.

i always thought of "java" as being a cup of tea

No, around these parts Java is always coffee. I think the shift from Java to 'joe' is correct.

Cup of Joe

Josephus Daniels (18 May 1862-15 January 1948) was appointed Secretary of the Navy by President Woodrow Wilson in 1913. Among his reforms of the Navy were inaugurating the practice of making 100 Sailors from the Fleet eligible for entrance into the Naval Academy, the introduction of women into the service, and the abolishment of the officers' wine mess. From that time on, the strongest drink aboard Navy ships could only be coffee and over the years, a cup of coffee became known as "a cup of Joe".

http://en.wiktionary.org/wiki/cup_of_joe

Oh yes.

As zomebody once zaid, data is not the plural of anecdote.

Cheer up, Mac. It's possible, you know, that although the phrase 'cup of joe' had been around for quite a while, Jesephus Daniels' edict helped to popularize it, while its putative antecedent 'cuppa Java' fell into relative disuse.