Hain Celestial (NASDAQ: HAIN), Annie's (NYSE: BNNY), and Whole Foods Market (NASDAQ: WFM) are three ways to clean up your portfolio as others clean up their lifestyle. One could be just right for healthy returns this year. But which one?

Hain is the mid-cap name, Whole Foods, of course, the big cap, and Annie's the small cap. Both Hain and Whole Foods Market have outperformed the S&P 500 over the last year, up 57.33% and 24.91% respectively.

Annie’s growth possibilities

Annie's was a hot ticket when it debuted in 2012, soaring 89% on its first trading day, and had risen to $52.38 in October but is now down 8% year over year. The company most recently disappointed on earnings thanks to higher commodity costs. Analysts are lukewarm to bullish with 7 Holds, 1 Buy, and 1 Strong Buy. Even with the pullback it is still rich with a 46.6 trailing earnings multiple.

Annie's has a line of 135 organic food items but 13 or less, or only 10%, are regularly carried in stores as CEO and co-Founder John Foraker said on the 2014 second quarter call. Getting out "key 33" products as well as new products in the pipeline is a strategic goal. Once these get into the 26,500 plus stores in the US and Canada they do very well as noted on the call.

The company is partly suffering from small cap growing pains with a need to expand number of store venues and better placement. While its macaroni and cheese category is growing stronger with more stores placing them in main aisles instead of "natural" aisle exile, the company has a lot of work ahead moving product to main aisles in mass, club, and grocery stores.

They are growing brand extensions and in 2014 expect to introduce another frozen brand building on the momentum of frozen pizza like the surprisingly popular macaroni and cheese pizza. Altogether the company has identified seven frozen categories worth $12 billion but has only rolled out the one.

Snacks are also a growing category and the company announced it had acquired its Joplin, MO cookie plant for $6 million. CEO Foraker said this should triple its snack production volume. This purchase will be mostly paid for with cash on hand and the company has no debt.

Growth by acquisition

Hain Celestial is much further along on its growth trajectory and is what Annie's could be in a decade or more with luck. In 2012 the company reported net sales of $1.378 billion, an increase of 24.3% year over year with a net income increase of 44%.

The bullish thesis on Hain aside from growing demand worldwide for natural and organic foods is its aggressive growth through acquisition. Hain now has 30 plus brands under its umbrella.

In 2012 Hain debuted 80 new products and acquired three foreign organic food companies, Daniels in the UK, Cully & Sully in Ireland, and Europe's Best in Canada.  These will help grow International Sales from its present 28% of sales. The company acquired five more companies in 2013: Sun Pat, Robertson's, BluePrint, Ella's Kitchen, and Hartley's and debuted 300 new products.

As the largest US producer of GMO-free food the company is benefiting from the public dialogue on GMOs along with General Mills’ decision to eliminate GMOs from Cheerios. Bears ask what's to keep customers from buying from the Big Boys of food if they all go GMO-free.  CEO Simon answered in a CNBC interview that these companies are taking baby steps and meanwhile, Hain is growing mind share and shelf space.

Hain Celestial is much further along on its growth trajectory and is what Annie's could be in a decade or more with luck. In 2012 the company reported net sales of $1.378 billion, an increase of 24.3% year over year with a net income increase of 44%. In 2013 sales increased to almost $2 billion.

The stock has pulled back from 52 week highs but is still rich with a 32.73 trailing earnings multiple.

Go with a grocer?

A different way to seek healthy returns rather than a manufacturer is Whole Foods Market.  However, grocery stores are well known for thin net profit margins.   While Whole Foods’ net profit margin at 4.23% is higher than Safeway (1.20%) it is not as high as Hain at 7.02% or Annie's at 7.43%.

Whole Foods is also trading at a rich multiple at 36.71 with a 0.9% yield compared to supermarket brethren like Safeway at 17 with a 2.0% yield. The bearish thesis on Whole Foods is organic share loss to Safeway and more importantly, Kroger, which may soon outstrip Whole Foods Market as largest natural foods grocer in the US. One bullish thesis is Whole Foods’ international expansion into the UK and Canada. Another is the global natural market pie is expected to reach $104.7 billion by 2015 at an annual compound growth rate of 12.9%.

Cutting the organic pie

Depending on your investment thesis, Annie’s has had a significant pullback and may have more upside than the other two. Hain Celestial, however, is acquisition hungry and this has been fueling its growth. As for Whole Foods Market, it does have a yield but seems to be in a lull compared to its earlier go-go years of growth.