I think the problem is that the linked paper only studied women for 12 months (try doing NFP for 10 years and saying it's effective) and they cherrypicked them too... normal cycles (!), partnered, specific age range, para 1 (!!!). That is definitely not going to match up with what NYT used and I wouldn't be surprised if any one of those points ends up making a difference.
I'm trying to get pregnant for the first time right now with still irregular cycles, and NFP for the purpose of pregnancy (educated, and I spend a LOT of time on a lot of communities about this) is a huge headache. There's no way I'd try this as birth control.
I can't speak to your experience, and as you say you have irregular cycles. BOM can actually be quite simple for many couples, STM a little less so since it tracks more fertility signs.
Here's a more recent report on a German study:
http://humrep.oxfordjournals.org/content/22/5/1310.short
"The STM is a highly effective family planning method, provided the appropriate guidelines are consistently adhered to."
Now, there is a true sense in which all NFP methods can be described as "rhythm" methods, i.e. human female fertility displays cyclic characteristics (generally speaking) between puberty and menopause, so methods which employ observation of a woman's fertility signs are tuning into the "rhythm" of her cycle.
But, "rhythm method" has become synonymous with Calendar Rhythm Method, the early-modern forms of which date back to the 1920s. The failure rate for typical use of historical rhythm method is higher than, say, the pill or condoms, and since the middle of the last century it has been dismissed as an effective form of birth control.
Several NFP methods developed since that time (mid 20th Century) involve more than marking days on a calendar. The woman, or the couple together, track one or more well-researched signs of fertility: basal body temperature, cervical mucus, changes in the cervix. Current and past observations are correlated according to straightforward rules to determine the start and end of a fertile period (i.e. "abstinence days" from vaginal intercourse, for those hoping to avoid pregnancy). So while days do get marked on a calendar, these methods are different enough in practice, and with respect to their effectiveness, that it's incorrect to lump them together with the older rhythm method. To avoid misperception, researchers themselves refer to these methods as FA, FAB, or FAM – "fertility awareness [based] [method/s]" – and not as "rhythm methods".
There is a true successor to the old calendar rhythm method. It was developed in the late 1990s and is called the Standard Days Method. See:
http://en.wikipedia.org/wiki/Calendar-based_contraceptive_me...
http://www.cyclebeads.com/research
As to the NYT's chart: as I said previously, I am a little dubious that it accurately reflects the worldwide data collected for the effectiveness of modern NFP. Which is not to say that I think the chart's creator is intentionally trying to mislead the Times' readership.
I have no comment on the effectiveness of modern IUDs, though I refer you to the German study I linked in a later comment above for additional info on NFP's effectiveness.
The larger point, sometimes missed by people who have a knee-jerk reaction to mention of NFP, is that its modern methods offer viable, drug-free, surgery-free, inexpensive approaches to birth control, which can be used effectively by rich and poor alike.
Cervical mucus that you gloss over involves sticking two digits way up your vagina every day and then evaluating the outcome. There's nothing wrong or gross about that but lots of people are unable to treat their own body with the required detachment.
I am aware of what is involved in tracking the various signs. Like most any voluntary human routine – exercise, special diet, regular study, etc. – the hardest part is in the beginning, i.e. making the commitment, getting in the habit, sticking to it. How difficult or easy it is to adopt an NFP tracking-routine is going to vary by the woman/couple. If for some women basal temperature and cervical mucus are perceived or prove to be difficult signs to track, for whatever reason, they could look into the Standard Days Method (linked above). Some may prefer that method in the first place.
http://www.lifeissues.net/writers/qia/qia_01nfpchina.html
"Due to its high efficacy, low expenditure and extreme safety incomparable by any other contraceptive methods, the BOM is well accepted by the Chinese couple of different cultural and economical backgrounds."
So, while I do not have enough background information on the chart provided by NYT, it doesn't seem to square with other known data.