Siphon is the common and preferred form
My very big dictionary (The American Heritage Dictionary of the English Language, 4th edition) contains no distinct entry for syphon. The entry for siphon reads as follows:
si-phon also sy-phon n. 1. A pipe or tube fashioned or deployed in an inverted U shape and filled until atmospheric pressure is sufficent to force a liquid from a reservoir in one end of the tube over a barrier higher than the reservoir and out the other end. 2. Zoology A tubular organ, especially of aquatic invertebrates such as squids or clams, by which water is taken in or expelled.
v. -phoned, -phon-ing, -phons -tr. To draw off or convey through as if through a siphon. -intr. To pass through a siphon.
adj. -si'phon-al, si-phon'ic
[Middle English, from Latin sipho, sipohon-, from Greek siphon.]
All of these variants use the siphon form where applicable, and while my keyboard doesn't translate the Latin and Greek characters properly, the way they are displayed in my book is visually similar to the letter I. The alternate spelling is listed as an alternate and then no further attention is paid to it. Study of additional dictionaries might be necessary to determine if this is standard or stylistic, but from the commentary I think we can safely determine that siphon is standard and syphon is an anomaly that no longer sees common use.
Of course, anomalous spelling can serve a stylistic or atmospheric function when used appropriately. I would recommend using siphon primarily and only using syphon when it serves a specific purpose.