You should definitely call the airline, especially if you want to be able to use the pump during the flight. My son uses a feeding pump, suction machine, ventilator and pulse oxymeter in flight. We have had to get all the items cleared by the airlines each time we have flown. Most airlines have a list of medical equipment approved for use in flight. Be sure to have your model number and the name and address of the manufacturer of the feeding pump on hand when you call the airline. Don't just speak to a ticket agent. Ask for special services. Most ticket agents do not have the authority to clear the medical items for use during flight. It is possible that you may be prohibited from using the feeding pump during take off and landing.
We have never had any problems getting through security with all of our son's medical equipment. As a matter of fact, in the major airports, the airline security people were familiar enough with medical equipment to ask me if we had a "breathing machine" in our carry on bag (I sent it through the x-ray but did not have a chance to tell them what it was until it had already gone through). All of this was before September 11, 2001. However, I would expect that the security folks are prepared to see some medical equipment. They may ask you to turn on the feeding pump to show it works (they do this with laptop computers sometimes).
I would definitely not check the feeding pump as baggage and I think that the airline would not want you to check it. They tell you not to check sensitive and expensive equipment.
When you call the airline, ask if there is any way someone can escort you through security.
We are planning to travel in late November. If you are traveling after that, let me know and I will tell you how it goes.