I used vcf-consensus (from VCFtools) to generate the variant FASTA sequence. The Haplotype can be specified using the -H parameter (as 1 or 2). The resulting FASTA file can be then used to extract the gene of interest.
FastaAlternateReferenceMaker performs one simple task.
It writes a fasta file in which reference SNP alleles are substituted with alternative SNP alleles. So, if your haplotypes do not coincide with the reference, it will not help you very much.
Luckily enough you can specify several intervals in which performing the task. So, you can first specify all the intervals (they can also be short, I think) in which haplotype A is coincident with the reference, and have the fasta of the haplotype B. Then, you can specify all the intervals in which the ahplotype B is equal to the reference and you will obtain the fasta of the haplotype A.
Man page is here, and the intervals can be specified with -L interval.file.name
It's tricky, but should work!