Yes there is an alternative... it is called a remap... and it is a better alternative.
Better is a relative term..
A remap (in theory) should be better tuned to your engine and more sympathetic to your requirements, however I'm not totally convinced on how "custom" most custom remaps are. There is a temptation surely to think that "this map worked in the last 14 JTD's, it should work on this one", and not take into account driving style, current & planned mileage, service schedule etc. This shouldn't be the case with most "reputable" tuners listed on these forums but after reading through a couple of hundred posts by owners with re-maps, there is only one or two guys on here I think really put (IMHO) the required effort into analysing each engine (and driver!) on a case by case basis. However, most tuners it would seem have their own rolling road or access to one so can't be beaten on pub bragging rights!
The box solution, whilst generic and not at all tuned to your car, does have a couple of advantages; many, like the box I'm opting for can be turned up or down depending on how much effect you're looking for. When I'm driving to the lakes for example, I don't really need it turned up to "11", I'm much more interested in the fuel economy. Conversely, If I'm going on a track day I DO want all available horses. Only a hardware box can do this, unless you want to get really friendly with your Tuner! The other advantage is that if/when I want to sell the car I can remove the box and sell it on. It is extremely unlikely that a prospective buyer would be interested in it. Again, you can't do this with a softmap, once you've spent the money, its gone.
Having researched it, there is no one correct answer, as per usual it is what is better for you.