As posted above, it has more to do with organization date of the companies. As a company went into service, it was assigned a number. That company number stayed with the company regardless of what station they are assigned to or re-assigned to. When Brooklyn was annexed, all new numbers were assigned. Brooklyn Engine 1 became Engine 201 of the NYFD (later FDNY) and Brooklyn Ladder 1 became Ladder 101. The stations have addresses, and other than being defined by the companies that are in the quarters, are not specifically designated units (i.e. station 1).
Throughout the northeast, this is the more common way that fire companies are numbered. Boston, Providence, Portland, ME, Manchester and Concord, NH, Worcester, Hartford, New Haven, Albany....etc. follow this rule, and I bet if you did some history research, your own county had something similar prior to a more recent (within the past 40 years) realignment where a uniform numbering system was implemented.
As was also stated above, the answer "because I said so" is also right, as it is a command level decision, and someone said that this is the way it's going to be. Based on the responses, it seems that some people don't want to accept that there are other numbering systems in use, and if it doesn't make sense to them, it's wrong....not the case.
EDIT
Off the top of my head, I can also point to Baltimore, Buffalo, Detroit, Memphis, Chicago, Washington DC, Wilmington, De, Philadelphia, Camden, NJ, Newark and Jersey City as places that follow the system of non-uniform company numbering, and I'm sure if I looked, I could come up with many more. It's just the way it's done in some places.