If you are looking for miRNA annotations based on homology to known miRNAs from other plants, you could try microHARVESTER, although I don't know if their web server it still running, it was down just now when I checked.

If you are looking for miRNA annotations from reference-aligned small RNA-seq data, there are lots of choices, including ShortStack, miRDeep-P, miRDeepFinder , and miRCAT

There are several tools, I have used before MiRanda http://www.microrna.org/microrna/getDownloads.do and psRNATarget http://plantgrn.noble.org/psRNATarget/

This site contains more programs -> http://mirnablog.com/microrna-target-prediction-tools/

I was just noticing in the new banana genome paper (the one with the Venn diagram everyone is talking about) had a link to a plant microRNA database and it has some prediction functions. http://bioinformatics.cau.edu.cn/PMRD/