Our research indicates that at least some wine experts are more discriminating than you and say that, even with the pump, the wine can “survive” only 3-5 days. For them, we imagine there would be significant loss to wait until the end of Shabbat. We will start our answer with their assumptions.
The Magen Avraham[2] discusses the case of meat that has not yet been kashered and is in need of washing before its deadline.[3] He posits that, in theory, if it were necessary to prevent loss, one would be allowed to rinse it on Shabbat without hachana being a problem. A source for this opinion is the halacha that one may move a non-muktzeh utensil on Shabbat to protect it from breakage or theft, even if he does not need it that day.[4]
In practice, however, the Magen Avraham forbids the rinsing, because even after the deadline has passed, one may still kasher the meat through broiling. Considering that some people prefer salting to broiling, we may infer from here that not all “losses” necessarily justify hachana. This, then, raises questions about maintaining the freshness of wine. On the other hand, there is certainly no requirement of total loss to justify taking steps on Shabbat. Even meat that can no longer be kashered at all can still be sold to a non-Jew, and yet were it not for the solution of broiling, rinsing would have been permitted. Therefore, those for whom their expensive wine will lose much of its value if they do not promptly pump the air out may do so on Shabbat.[5]
Let us now consider your question from the perspective of someone like you, for whom waiting until after Shabbat is not significant. As a contrary example, consider that a husband may revoke his wife’s oaths on Shabbat only because it will be too late to do so if he waits until after Shabbat.[6] In general, when there is an alternative way to avoid a loss that can be done after Shabbat, one must wait.[7] We do not find a halachic precedent that, under normal circumstances, one’s concern that he might forget to take care of something if he waits until after Shabbat is sufficient to justify doing the preparatory work on Shabbat.
Nevertheless, there are a few ideas that might justify pumping on Shabbat. The Orchot Shabbat[8] maintains that an action whose only purpose is to prevent a loss is totally divorced from any issue of hachana. (He explains that in the case of rinsing the meat, we require alternatives because rinsing has a positive element to it other than avoiding loss.) Thus, in your case, you could claim that since one pumps only to avoid loss, it does not matter that you can do it after Shabbat.
Another possible leniency is based on a rule championed by Rav S.Z. Auerbach and cited by several contemporary works.[9] Actions that a person does naturally, as a matter of course – without specific thought of doing it now in order to save time later – are permitted even if the results are meant for only after Shabbat. Some examples are taking home one’s tallit and siddur after shul and putting food in the refrigerator. These actions are considered finishing off the previous usage. While pumping air from a wine bottle seems to me to be a deliberate action with a clear thought process, perhaps it can be argued that for serious wine connoisseurs, it is as natural as replacing the cap on a soda bottle.
In summation, those who deem that delaying pumping the air will cause a real loss are permitted to pump the air from a wine bottle on Shabbat. Other users have what to rely upon if they prefer not to wait. The strength of the leniency may depend on the level of their discrimination and the extent to which pumping is a standard, almost trivial action.