How to compute LD for pairs of variants with Plink
Yes, you can do this with plink.  

You can use the flag --ld-snp &lt;variant_id&gt; to calculate LD between your SNP of interest and all other SNPs.
If you have multiple SNPs of interest, and want each of those compared with every SNP in your dataset, use --ld-snps &lt;snp1-snp100,snp102,snp104&gt;
A final option to calculate LD between a specific pair of SNPs is --ld &lt;variant_id1&gt; &lt;variant_id2&gt;  

This the relevant plink manual page