Usage of the word pip meaning "seed" dates back to around 1797. It originates from the word "Pippin" (a very old word for apple). The only difference in meaning between the words seed and pip seems to be that pips only come from fruit.
An Example
When comparing the fruits of Europe to those of America, Thomas Jefferson wrote from Paris, "They have no apples here to compare with our Pippin."
As a note: Jefferson was actually referring to the Newton Pippin specifically, rather than all pippins.
Things with pips:
A little background:
A pip is a fertilised and ripened ovule, made up of the plant embryo, some stored food (for the plant to grow), and a protective outer coat. Pip-bearing plants are the highest in the evolutionary scale (of plants). In lower plants (mosses and ferns) spores are utilised to spread new plants. Long dormancy in some pips is made possible by their firm outer layer, which has to be scratched or split to force sprouting. In plant breeding circles, the source of pollen for fertilization is carefully controlled to produce the desired qualities in the pips. Under natural conditions a plant grown from pips may be quite different genetically from its maternal plant.