Transgender Support Group
This community is here to support and help the large population of transgender people. If you or anyone you know identify as transgender, this is the place to share your feelings and experiences and speak with others who are going through similar things in their lives.

As far as your school councilor.... I have never met one that has EVER had much of a clue, but if you must talk to them, then when they say it is a phase ask them what degree and license they have to make such a diagnosis, if they have none, well there is your answer on how helpful they will be to you. My personal suggestion on this is to find a therapist and go. Find one with some experience in the matter and go see them. With what I know of Medical care in Canada, they will set you up with someone who can help you.
There are a couple ways to handle what you are going through (which is complicated by age relation to puberty and school and so on). The first is you can take someone calling you she as a personal attack, in which case it will have a bite and sting. This generally means that you have not made being trans part of who you are and thus people can use it to hurt you. Or you can take it and make it part of you and when they say she, you understand that they don't know you, they don't know your situation, they need to rewrite an entire life knowing you and they are reacting to the shell you were plopped into. In this case, you have an understanding that not everyone is going to know what you are going through since you have not told them and even if you have, you have known this person how long and how many memories and years to they have to overwrite to get it correct? That said, them saying it will hurt much less in this instance. Not sure if this helps you, but it is the advice I can give.
The alternative is to stay with things like they are and that is clearly not working for you.
If I get a vote, I say give him a chance to know what a great guy you really are, and hopefully he's a good enough guy for you. If not, betterto find out ssooner than later. Plenty of fish in the sea.
As far as your boyfriend? I understand that. I have hid my true gender from boyfriends in the past. I lied to their families, my family, everyone. Everyone just assumed I "crossdressed." It really hurt to feel not accepted. But the truth is, there are people out there who will accept you and love you as you are. Male or female. It doesn't matter. It can take time finding them, but they are there.
I think you need to have a nice sit down talk with your boyfriend and tell him the truth. If he doesn't accept you, then he isn't good enough. There is someone better out there for you. If you want a relationship I would suggest OkCupid because they allow you to list yourself as Transgender rather than just male or female.
But first and foremost is accepting yourself and loving yourself. =)
You can do it. Just remember your happiness comes first and if someone doesn't understand that then they are the one with the problem.