(a)+(b)[1]: I like tea, especially chamomile tea; however, I prefer coffee.
This is the most correct form. Another alternative is to move "especially chamomile tea" into parentheses:
I like tea (especially chamomile); however, I prefer coffee.
You can also move "however":
I like tea (especially chamomile); I, however, prefer coffee.
But the most condensed form is to replace "however, I" with "but":
I like tea (especially chamomile) but prefer coffee.
I like tea, especially chamomile, but prefer coffee.
But if you want to keep the original forms as much as possible, than (a)+(b)[1] is most correct.
(a)+(b)[2]: I like tea, especially chamomile tea, however, I prefer coffee.
This sentence is really hard to read because there are so many commas. It is also less correct because there is no conjunction between "I like tea" and "I prefer coffee". In informal speech, you can use "however" as a conjunction but I would caution against it in writing.
(a)+(b)[3]: I like tea, especially chamomile tea,; however, I prefer coffee.
This is incorrect. English does not use the punctuation pattern of ",;".
I have a feeling that (a)+(b)[1] is correct; however, I'm not really sure what rule would govern that. Is there some precendence rule making a semicolon 'trump' a comma?
The rule governs the combining of clauses without using a conjunction. You could use any of the following:
(1) I like tea and I like coffee
(2) I like tea but I prefer coffee
(3) I like tea; however, I prefer coffee
(4) I like tea; I prefer coffee
But you typically wouldn't use:
(5) I like tea, I prefer coffee
(6) I like tea, however, I prefer coffee